acii (New England Biolabs)


Name:
AciI
Description:
AciI 1 000 units
Catalog Number:
R0551L
Price:
282
Category:
Restriction Enzymes
Size:
1 000 units
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Structured Review

AciI 1 000 units
https://www.bioz.com/result/acii/product/New England Biolabs
Average 95 stars, based on 1 article reviews
Price from $9.99 to $1999.99
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1) Product Images from "The 2HA line of Medicago truncatula has characteristics of an epigenetic mutant that is weakly ethylene insensitive"
Article Title: The 2HA line of Medicago truncatula has characteristics of an epigenetic mutant that is weakly ethylene insensitive
Journal: BMC Plant Biology
doi: 10.1186/1471-2229-14-174

Figure Legend Snippet: Analysis of DNA methylation. (a) Amplified methylation polymorphism (AMP) profiling. DNA from two biological replicates (lanes) was used for AMP before (on the left) or after (right) digestion with HpaII. Arrows point to the differences in methylation between 2HA and Jemalong. (b, c) Analysis of MtEIL1 methylation. (b) The MtEIL1 gene and promoter. Vertical bars depict positions of AciI cut sites, and bisulphate sequenced regions also indicated. After digestion of genomic DNA by AciI, qPCR was performed with primers F2/R2 and F4/R4 separately. (c) qPCR results show amount of undigested DNA due to methylation of digestion sites. Results are mean ± SE of 4 repeats.
Techniques Used: DNA Methylation Assay, Amplification, Methylation, Real-time Polymerase Chain Reaction
2) Product Images from "Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells"
Article Title: Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells
Journal: Nucleic Acids Research
doi: 10.1093/nar/gkx026

Figure Legend Snippet: Schematic representation of CGI-seq. TEST: single cell being studied. Methylation control (MC): cells that are used to define the detectable CGIs or any other accessible methylated regions (AMRs), sharing the same genome as the TEST. For CGI-seq analysis, the genomic DNA is classified into three classes of sequences: Me-CGIs (representing methylated CGIs, and more generally, Me-AMRs) indicated as a red line, Um-CGIs (unmethylated CGIs, and generally Um-AMRs) indicated as a blue line and undetectable regions indicated as a black line. Green lines are amplified sequences. Solid dot: Me-CpG sites. Hollow dot: Um-CpG sites. The intact gDNA is released from cell (step 1) and digested with RE1 (TEST) or no digestion (MC) (step 2), followed by MDA amplification (step 3). The amplification product is then digested by RE2 (step 4), in which the short fragments are converted t‘o a library and subjected to massive sequencing (step 5). The reads are aligned to the genome (step 6) and the methylation status of the AMRs (particularly CGIs) is determined (‘Materials and Methods’ section). The AMRs detected in both the TEST and the MC are called Me-CGIs (or Me-AMRs). The AMRs uniquely detected in the MC but not in the TEST are called Um-CGIs (or Um-AMRs) of the TEST. RE1 (four MREs in combination: Cfr42I (SacII), PdiI (NaeI), Eco52I (EagI) and PteI(BssHII), FastDigest enzyme from Thermal Scientific Inc.) distinguishes Me-CGIs (Me-AMRs) from Um-CGIs (Um-AMRs). MDA selectively depletes Um-CGIs (Um-AMRs) of the TEST and amplifies Me-CGIs (Me-AMRs). RE2 (either BstUI alone, or a combination of 3 separate REs (ABH: AciI, BstUI and Hinp1I from NEB)) generates fragments specifically enriching CGI sequences (and other CG-rich regions) from non-CGI sequences.
Techniques Used: Methylation, Amplification, Multiple Displacement Amplification, Sequencing
3) Product Images from "Hose in Hose, an S locus-linked mutant of Primula vulgaris, is caused by an unstable mutation at the Globosa locus"
Article Title: Hose in Hose, an S locus-linked mutant of Primula vulgaris, is caused by an unstable mutation at the Globosa locus
Journal: Proceedings of the National Academy of Sciences of the United States of America
doi: 10.1073/pnas.0910955107

Figure Legend Snippet: Retrotransposon excision is associated with demethylation of the PvGlo locus. ( A ) Organization of wild-type, transposon, and revertant alleles of PvGlo showing location of upstream methylation-sensitive AciI restriction enzyme sites. The PvGlo -specific primers (F1, R1, R3) and transposon-specific PCR primers (R2, F2) are indicated. The retrotransposon insertion site is shown (-723); LTRs are shown in gray. ( B ) Methylation-sensitive PCR analysis of the wild-type, transposon, and revertant alleles of PvGlo using allele-specific primer combinations as indicated. Primer specificity is demonstrated on DNA from leaves of wild-type (wt) and homozygous Hose in Hose (HH) plants. DNA samples from whorl-1 tissue or combined whorl-2, -3, and -4 tissue from revertant (R), semirevertant (SR), and Hose in Hose (H) flowers from the same plant were either digested with Aci1 or uncut as indicated before PCR amplification using allele-specific primer combinations as shown before fractionation by agarose gel electrophoresis. The different alleles amplified by each primer combination are indicated and the excision allele-specific PCR product is highlighted (*). PCR products generated from uncut genomic DNA that are absent after predigestion with AciI reveal unmethylated sites.
Techniques Used: Methylation, Polymerase Chain Reaction, Amplification, Fractionation, Agarose Gel Electrophoresis, Generated
4) Product Images from "Epigenetic regulation of matrix metalloproteinase expression in ameloblastoma"
Article Title: Epigenetic regulation of matrix metalloproteinase expression in ameloblastoma
Journal: BMC Clinical Pathology
doi: 10.1186/1472-6890-12-11

Figure Legend Snippet: Representative figure of the methylation analysis. A : Methylation status of MMP-2 in ameloblastoma. M: PCR products when amplified by methylated primers (205 bp); U: PCR products when amplified by unmethylated primers (206 bp); +M: positive control for methylated reaction; +U: positive control for unmethylated reaction. -M and -U: negative controls without DNA. Lines 1 to 3 represent DNA from ameloblastoma samples. B : Methylation status of MMP-9 in ameloblastoma. DNA samples were digested by the AciI restriction enzyme followed by PCR, flanking the restriction sites. Absent band indicates unmethylated profile (U) due to DNA cleavage by the restriction enzyme. Presence of the PCR band represents methylated profile (M) of the MMP-9 gene. +M: methylated positive control; +U: unmethylated positive control; - : negative control without DNA.
Techniques Used: Methylation, Polymerase Chain Reaction, Amplification, Positive Control, Negative Control
5) Product Images from "How to Isolate a Plant's Hypomethylome in One Shot"
Article Title: How to Isolate a Plant's Hypomethylome in One Shot
Journal: BioMed Research International
doi: 10.1155/2015/570568

Figure Legend Snippet: Complementary identification of genomic regions in rice due to restriction site locations. A detailed representation of the mapping results is shown for both enzymes, AciI and HpaII. The identified regions around the displayed gene differ due to the lack of recognition sites for the other enzyme. On the right, an example for overlapping but expanded regions is given.
Techniques Used:

Figure Legend Snippet: Length distribution of genomic regions identified for AciI, HpaII, and the combined dataset in rice. The length distribution of hypomethylated regions identified with the three datasets up to the maximal length is shown as well as a closer view to the region between 0 and 2.000 bp, where an increase in length is visible for the combined dataset. Additionally, the amount of regions, the average and maximum length, and the average reads per region are given.
Techniques Used:

Figure Legend Snippet: Genes and transposable elements identified in the rice genome with the methyl filtration technique. The regions comprised of at least five reads (left), and all regions (middle) show a clear depletion of transposable elements for AciI, Bsh1236I, and HpaII. On the right a representation of genes and transposable elements is given showing potential methylation sites within their gene space. All values are shown in percent based on the annotated 39.954 genes and 15.847 transposable elements.
Techniques Used: Filtration, Methylation
6) Product Images from "Selective amplification of hypermethylated DNA from diverse tumor types via MSRE-PCR"
Article Title: Selective amplification of hypermethylated DNA from diverse tumor types via MSRE-PCR
Journal: Oncotarget
doi: 10.18632/oncotarget.27825

Figure Legend Snippet: Methylation sensitive restriction sites in target cDMRs. Five MSREs are considered here: HhaI, HpaII, HpyCH4IV, AciI and BstUI. ( A ) Histogram of the number of MSRE sites in the target regions. ( B ) Scatterplot of the number of MSRE sites versus the number of CpGs in the target regions showing a linear relationship (R 2 = 0.89, p
Techniques Used: Methylation
7) Product Images from "Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease"
Article Title: Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease
Journal: PLoS ONE
doi: 10.1371/journal.pone.0194036

Figure Legend Snippet: Schema of methylation-sensitive SNP array. If allele-specific DNA methylation (ASM) around heterozygous SNP A/C exists (which is hypermethylated around A allele and hypomethylated around C allele), SNP is called A/C in micro array before digestion and A/A after digestion by MSREs. Thus, the probes heterozygous in uncut genomic DNA and homozygous in MSREs-digested DNA indicate ASM around SNP. Because we expect methylation skew between two alleles, all heterozygous SNPs which the ratio of signal intensities given two alleles changed after digestion should be extracted. SNP, single-nucleotide polymorphisms; MSREs, methylation-sensitive restriction enzymes, which contain HpaII ( 5′-CˆCGG-3′ ), HhaI ( 5′-GCGˆC-3′ ), and AciI ( 5′-CˆCGC-3′ ).
Techniques Used: Methylation, DNA Methylation Assay, Microarray
8) Product Images from "Genetic and Physical Mapping of DNA Replication Origins in Haloferax volcanii"
Article Title: Genetic and Physical Mapping of DNA Replication Origins in Haloferax volcanii
Journal: PLoS Genetics
doi: 10.1371/journal.pgen.0030077

Figure Legend Snippet: DNA Replication Origin on Contig 454 Is on Chromosomes pHV1 and pHV4 (A) Sequence features of the ARS element isolated from genomic libraries of WR340 DNA. Coordinates of plasmid inserts generated by HpaII and AciI digestion are shown (including insert in pTA194), in addition to the minimal ARS element determined by AciI digestion (in pTA250) or PCR amplification (in pCN12). Numbering refers to TIGR contig 454 (pHV1). (B) Sequence of repeats found at the intergenic region of the pHV1/4 replication origin (correspond to numbered arrows in Figure 1 A). Orientation is indicated by arrows (righthand side) and conserved sequences are shaded. Six of the 13 repeats feature a complete ORB element (boxed), while a core mini-ORB element is conserved in all repeats. The sequence motif found in repeats surrounding the DUE is indicated by the dashed box. (C) Southern blot of PFG of intact DNA from strains H53 and H230, probed with HpaII ARS insert from pTA194, or intergenic region replaced by trpA in pTA266 (see Figure 1 D). (D) Intergenic region of ori-pHV1/4 was replaced by trpA marker by using the deletion construct pTA266. H. volcanii H53 was transformed with pTA266 to generate H220, which was used to derive the pHV1/4 origin deletion strain H230. Predicted fragment sizes of StuI digest are indicated. (E) StuI digest of genomic DNA from strains H53, H220, and H230, probed with DNA flanking the intergenic region. The band indicated * represents episomal DNA carrying the pHV1/4 origin, resulting from excision of the integrated plasmid.
Techniques Used: Sequencing, Isolation, Plasmid Preparation, Generated, Polymerase Chain Reaction, Amplification, Southern Blot, Marker, Construct, Transformation Assay

Figure Legend Snippet: DNA Replication Origin on the Main Chromosome: oriC1 (A) Sequence features of the ARS element isolated from genomic libraries of H230 DNA, including selected genes (see text for details). Coordinates of plasmid inserts generated by AciI digestion are shown (including insert in pTA313), in addition to the minimal ARS element in pTA441 and pCN11. See Figure 1 A for key. Numbering refers to TIGR contig number 455. Main chromosome, Chr. (B) Above the line are sequences of repeats found at the intergenic region of the H. volcanii chromosomal replication origin (correspond to numbered arrows in Figure 2 A). Below the line are sequences of repeats found at other (presumed) archaeal origins. The species and relevant cdc6/orc1 genes are H. marismortui cdc6–4 (Hmar-1–2), Halobacterium sp. NRC-1 orc7 (NRC1-1-2), Natronomonas pharaonis cdc6–1 (Npha-1–2), S. solfataricus cdc6–1 (Sso-1–2), and P. abyssi cdc6 (Pab-1–4). The orientation is indicated by arrows and conserved positions are shaded. Among halophilic archaea, repeats surrounding the primary DUE feature a longer consensus sequence (Halo-ORB, boxed), which contains the core mini-ORB and “G-string” elements also found in other archaea, plus a halophile-specific “G-string.” (C) Southern blot of PFG of DNA from strain H53, probed with the AciI ARS insert from pTA313.
Techniques Used: Sequencing, Isolation, Plasmid Preparation, Generated, Southern Blot
9) Product Images from "Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease"
Article Title: Allele-specific DNA methylation of disease susceptibility genes in Japanese patients with inflammatory bowel disease
Journal: PLoS ONE
doi: 10.1371/journal.pone.0194036

Figure Legend Snippet: Schema of methylation-sensitive SNP array. If allele-specific DNA methylation (ASM) around heterozygous SNP A/C exists (which is hypermethylated around A allele and hypomethylated around C allele), SNP is called A/C in micro array before digestion and A/A after digestion by MSREs. Thus, the probes heterozygous in uncut genomic DNA and homozygous in MSREs-digested DNA indicate ASM around SNP. Because we expect methylation skew between two alleles, all heterozygous SNPs which the ratio of signal intensities given two alleles changed after digestion should be extracted. SNP, single-nucleotide polymorphisms; MSREs, methylation-sensitive restriction enzymes, which contain HpaII ( 5′-CˆCGG-3′ ), HhaI ( 5′-GCGˆC-3′ ), and AciI ( 5′-CˆCGC-3′ ).
Techniques Used: Methylation, DNA Methylation Assay, Microarray
10) Product Images from "Molecular Identification of Mucor and Lichtheimia Species in Pure Cultures of Zygomycetes"
Article Title: Molecular Identification of Mucor and Lichtheimia Species in Pure Cultures of Zygomycetes
Journal: Jundishapur Journal of Microbiology
doi: 10.5812/jjm.35237

Figure Legend Snippet: Agarose Gel Electrophoresis of 18sS rRNA PCR Products of Different Mucorals After Restriction Digestion With XmnI and AcII Lanes 12, 11, 10, 9, 8, 2 and 13, M. circinelloides , M. racemosus , M. ramosissimus or M. plumbeus ; Lanes 3, 1, 7, 6, 5, 4, and 14, L. corymbifera or L. blakesleeana ; N, negative control; M, 100 bp molecular size marker.
Techniques Used: Agarose Gel Electrophoresis, Polymerase Chain Reaction, Negative Control, Marker
11) Product Images from "Epstein-Barr Virus Rta-Mediated Accumulation of DNA Methylation Interferes with CTCF Binding in both Host and Viral Genomes"
Article Title: Epstein-Barr Virus Rta-Mediated Accumulation of DNA Methylation Interferes with CTCF Binding in both Host and Viral Genomes
Journal: Journal of Virology
doi: 10.1128/JVI.00736-17

Figure Legend Snippet: EBV Rta expression increases DNA methylation and decreases CTCF binding in the promoter regions of MYC , CCND1 , and JUN . (A, left) Schematic diagrams of methylation-sensitive restriction enzyme sites, CTCF binding sites, and Rta binding sites in each target promoter region. These regions contain no EcoRI site, thus EcoRI served as an input control for AciI, HpaII, and HinP1I. The MYC gene body without Rta and CTCF binding sites served as a negative control (N.C.). Lengths of promoters are illustrated to scale. (Right) CpG methylation levels in the cellular promoters of 293TetLuc and 293TetER cells. Cellular DNAs of paired untreated and doxycycline (Dox)-treated (12 and 24 h) cells were extracted and subjected to restriction enzyme digestions. DNA fragments protected by each methylation-sensitive enzyme were quantified by real-time PCR. Fold changes of each restriction enzyme assessment denote the relative CpG methylation levels in the Dox-treated cells compared to their untreated counterparts. Error bars depict the means ± SD from four independent experiments. Student's t test was used to evaluate the significant difference between the indicated data set. ***, P
Techniques Used: Expressing, DNA Methylation Assay, Binding Assay, Methylation, Negative Control, CpG Methylation Assay, Real-time Polymerase Chain Reaction
12) Product Images from "Comparison of Bacteroides-Prevotella 16S rRNA Genetic Markers for Fecal Samples from Different Animal Species"
Article Title: Comparison of Bacteroides-Prevotella 16S rRNA Genetic Markers for Fecal Samples from Different Animal Species
Journal: Applied and Environmental Microbiology
doi: 10.1128/AEM.71.10.5999-6007.2005

Figure Legend Snippet: Examples of T-RFLP peaks resulting from cow and human fecal samples cut with AciI, MspI, and HaeIII.
Techniques Used:
Related Articles
Methylation:Article Title: The 2HA line of Medicago truncatula has characteristics of an epigenetic mutant that is weakly ethylene insensitive Article Snippet: The Amplified methylation polymorphism (AMP) protocol for arbitrarily detecting DNA methylation variation in genomic DNA was that described in [ ]. .. To test for differential methylation within MtEIL1 in 2HA and Jemalong e.g. [ ], DNA (10 μg) was digested overnight by Article Title: Hose in Hose, an S locus-linked mutant of Primula vulgaris, is caused by an unstable mutation at the Globosa locus Article Snippet: PvGlo promoter sequences were obtained from wild-type and Hose in Hose homozygote and heterozygote plants using a Genome Walker Kit (Clontech). .. For PCR and methylation analysis, genomic DNA (1 μg) was digested overnight with 20 U Polymerase Chain Reaction:Article Title: The 2HA line of Medicago truncatula has characteristics of an epigenetic mutant that is weakly ethylene insensitive Article Snippet: The Amplified methylation polymorphism (AMP) protocol for arbitrarily detecting DNA methylation variation in genomic DNA was that described in [ ]. .. To test for differential methylation within MtEIL1 in 2HA and Jemalong e.g. [ ], DNA (10 μg) was digested overnight by Article Title: Hose in Hose, an S locus-linked mutant of Primula vulgaris, is caused by an unstable mutation at the Globosa locus Article Snippet: PvGlo promoter sequences were obtained from wild-type and Hose in Hose homozygote and heterozygote plants using a Genome Walker Kit (Clontech). .. For PCR and methylation analysis, genomic DNA (1 μg) was digested overnight with 20 U Incubation:Article Title: Modulation of Enhancer Looping and Differential Gene Targeting by Epstein-Barr Virus Transcription Factors Directs Cellular Reprogramming Article Snippet: Triton X-100 was then added to the nuclei to give a final concentration of 2% and the samples incubated for 1 hr at 37°C with shaking. .. 400 U EcoR I-HF, Hind III or Article Title: Considerations When Analyzing the Methylation Status of PTEN Tumor Suppressor Gene Article Snippet: .. Three hundred nanograms of genomic cell line DNA was incubated with 10 units of Sequencing:Article Title: Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells Article Snippet: The sizes of PCR products and the sequences of primers used are the following: CGP1, 160 bp, TCACTGCAAGCTCTGCCTCT, CGGATCACGAGGTCAGAAGA; CGP2, 178 bp, CATGCCTATAACCCCAGCAC, ATTCTCCTGCCTCAGCCTCT; CGN1 (with gene C19), 185 bp, TAGACCGGGGTCGGGACAGGA, TGCCCGACAGGGCGTGTTTGA; CGN2 (with gene ACTB), 221bp, GTGGACATCTCTTGGGCACT, GACCCACCCAGCACATTTAG. .. Library construction for reduced representation sequencing To enrich the sequences for CGIs and other CpG-rich regions, 1.5 μg of amplified DNA from each sample was divided into three equal amounts and digested by one of the three RE2 reagents respectively: Amplification:Article Title: Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells Article Snippet: The sizes of PCR products and the sequences of primers used are the following: CGP1, 160 bp, TCACTGCAAGCTCTGCCTCT, CGGATCACGAGGTCAGAAGA; CGP2, 178 bp, CATGCCTATAACCCCAGCAC, ATTCTCCTGCCTCAGCCTCT; CGN1 (with gene C19), 185 bp, TAGACCGGGGTCGGGACAGGA, TGCCCGACAGGGCGTGTTTGA; CGN2 (with gene ACTB), 221bp, GTGGACATCTCTTGGGCACT, GACCCACCCAGCACATTTAG. .. Library construction for reduced representation sequencing To enrich the sequences for CGIs and other CpG-rich regions, 1.5 μg of amplified DNA from each sample was divided into three equal amounts and digested by one of the three RE2 reagents respectively: |