aci i  (New England Biolabs)


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    Name:
    AciI
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    AciI 1 000 units
    Catalog Number:
    r0551l
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    282
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    1 000 units
    Category:
    Restriction Enzymes
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    Structured Review

    New England Biolabs aci i
    AciI
    AciI 1 000 units
    https://www.bioz.com/result/aci i/product/New England Biolabs
    Average 99 stars, based on 34 article reviews
    Price from $9.99 to $1999.99
    aci i - by Bioz Stars, 2020-09
    99/100 stars

    Images

    1) Product Images from "Isolation of Bartonella henselae and Two New Bartonella Subspecies, Bartonellakoehlerae Subspecies boulouisii subsp. nov. and Bartonella koehlerae Subspecies bothieri subsp. nov. from Free-Ranging Californian Mountain Lions and Bobcats"

    Article Title: Isolation of Bartonella henselae and Two New Bartonella Subspecies, Bartonellakoehlerae Subspecies boulouisii subsp. nov. and Bartonella koehlerae Subspecies bothieri subsp. nov. from Free-Ranging Californian Mountain Lions and Bobcats

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0148299

    PCR-RFLP of a gltA gene fragment using the restriction endonuclease Aci I. Lanes 1, 4 and 19 show 100 BP Ladder; Lane 2, Mt Lion L27-96; Lane 3, Mt Lion L42-94; Lane 5, Mt Lion L-39-97; Lane 6, Mt Lion FM98061; Lane 7, Bobcat L08-96; Lane 8, Bobcat L17-96; Lane 9, Bobcat DS08; Lane 10, Bobcat L10-97; Lane 11, Bobcat L11-97; Lane 12, Bobcat SC443; lane 13, Bobcat DS507; Lane 14, B . henselae Type I; Lane 15, B . henselae Type II; Lane 16, B . clarridgeiae ; Lane 17, B . koehlerae ; Lane18, B . bovis (“weissii” isolate).
    Figure Legend Snippet: PCR-RFLP of a gltA gene fragment using the restriction endonuclease Aci I. Lanes 1, 4 and 19 show 100 BP Ladder; Lane 2, Mt Lion L27-96; Lane 3, Mt Lion L42-94; Lane 5, Mt Lion L-39-97; Lane 6, Mt Lion FM98061; Lane 7, Bobcat L08-96; Lane 8, Bobcat L17-96; Lane 9, Bobcat DS08; Lane 10, Bobcat L10-97; Lane 11, Bobcat L11-97; Lane 12, Bobcat SC443; lane 13, Bobcat DS507; Lane 14, B . henselae Type I; Lane 15, B . henselae Type II; Lane 16, B . clarridgeiae ; Lane 17, B . koehlerae ; Lane18, B . bovis (“weissii” isolate).

    Techniques Used: Polymerase Chain Reaction

    2) Product Images from "Modulation of Enhancer Looping and Differential Gene Targeting by Epstein-Barr Virus Transcription Factors Directs Cellular Reprogramming"

    Article Title: Modulation of Enhancer Looping and Differential Gene Targeting by Epstein-Barr Virus Transcription Factors Directs Cellular Reprogramming

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1003636

    The influence of EBNA 3C on chromosome looping at the ADAM28/ADAMDEC1 locus. (A) Diagram (not to scale) showing the Hind III restriction fragments around the ADAM28 locus that encompass the promoter (P), the ADAM enhancer (E, located downstream of ADAM28 ) and two intervening control regions (con1 and con2). The arrow indicates the direction of transcription. (B) Chromosome conformation analysis of the ADAM28 locus in the pz1 control BJAB cell line (−) and the E3C-3 stable EBNA 3C expressing cell line (+) using primer pairs that amplify across promoter-enhancer or promoter-control ligation junctions. Positive controls show PCR amplification from control digestion and ligation reactions carried out using PCR-amplified DNA fragments encompassing the promoter, enhancer and control regions. (C) Diagram (not to scale) showing the Aci I restriction fragments around the ADAMDEC1 locus that encompass the promoter (P), the ADAM enhancer (E, located upstream of ADAMDEC1 ) and an intervening control region (con). The arrow indicates the direction of transcription. (D) Chromosome conformation analysis of the ADAMDEC1 locus in the pz1 control BJAB cell line (−) and the E3C-3 stable EBNA 3C expressing cell line (+) using primer pairs that amplify across promoter-enhancer or promoter-control ligation junctions. Positive controls show PCR amplification from control digestion and ligation reactions carried out using PCR-amplified DNA fragments encompassing the promoter, enhancer and control region.
    Figure Legend Snippet: The influence of EBNA 3C on chromosome looping at the ADAM28/ADAMDEC1 locus. (A) Diagram (not to scale) showing the Hind III restriction fragments around the ADAM28 locus that encompass the promoter (P), the ADAM enhancer (E, located downstream of ADAM28 ) and two intervening control regions (con1 and con2). The arrow indicates the direction of transcription. (B) Chromosome conformation analysis of the ADAM28 locus in the pz1 control BJAB cell line (−) and the E3C-3 stable EBNA 3C expressing cell line (+) using primer pairs that amplify across promoter-enhancer or promoter-control ligation junctions. Positive controls show PCR amplification from control digestion and ligation reactions carried out using PCR-amplified DNA fragments encompassing the promoter, enhancer and control regions. (C) Diagram (not to scale) showing the Aci I restriction fragments around the ADAMDEC1 locus that encompass the promoter (P), the ADAM enhancer (E, located upstream of ADAMDEC1 ) and an intervening control region (con). The arrow indicates the direction of transcription. (D) Chromosome conformation analysis of the ADAMDEC1 locus in the pz1 control BJAB cell line (−) and the E3C-3 stable EBNA 3C expressing cell line (+) using primer pairs that amplify across promoter-enhancer or promoter-control ligation junctions. Positive controls show PCR amplification from control digestion and ligation reactions carried out using PCR-amplified DNA fragments encompassing the promoter, enhancer and control region.

    Techniques Used: Expressing, Ligation, Polymerase Chain Reaction, Amplification

    3) Product Images from "Molecular detection of the G(-248)A BAX promoter nucleotide change in B cell chronic lymphocytic leukaemia"

    Article Title: Molecular detection of the G(-248)A BAX promoter nucleotide change in B cell chronic lymphocytic leukaemia

    Journal: Molecular Pathology

    doi:

    Restriction enzyme analysis and parallel direct sequencing of polymerase chain reaction (PCR) products. (A) Aci I and (B) Tau I endonuclease cleavage followed by 10% polyacrylamide gel analysis. M, molecular weight marker, 100 bp DNA ladder (Gibco BRL, Burlington, Ontario, Canada). (A) Lane 1, chronic lymphocytic leukaemia (CLL) sample 1, amplified BAX promoter segment before digestion; lanes 2–5, PCR products digested with Aci I; lane 2, CLL sample 2 with a heterozygous single nucleotide polymorphism (SNP); lanes 3 and 4, CLL samples 3 and 4 with no SNP; lane 5, RL cell line with homozygous SNP. (B) PCR products digested with Tau I; lane 2, CLL sample 2 with a heterozygous SNP; lane 3, CLL sample 3 with no SNP; lane 5, RL cell line with homozygous SNP. (C) Left hand column: direct sequence of the BAX promoter region. The control sample (I) shows no alteration, whereas a CLL sample (II) shows a heterozygous SNP, and the RL cell line (III) has a homozygous SNP. Middle and right hand columns: corresponding samples digested with the Aci I and Tau I enzymes, respectively
    Figure Legend Snippet: Restriction enzyme analysis and parallel direct sequencing of polymerase chain reaction (PCR) products. (A) Aci I and (B) Tau I endonuclease cleavage followed by 10% polyacrylamide gel analysis. M, molecular weight marker, 100 bp DNA ladder (Gibco BRL, Burlington, Ontario, Canada). (A) Lane 1, chronic lymphocytic leukaemia (CLL) sample 1, amplified BAX promoter segment before digestion; lanes 2–5, PCR products digested with Aci I; lane 2, CLL sample 2 with a heterozygous single nucleotide polymorphism (SNP); lanes 3 and 4, CLL samples 3 and 4 with no SNP; lane 5, RL cell line with homozygous SNP. (B) PCR products digested with Tau I; lane 2, CLL sample 2 with a heterozygous SNP; lane 3, CLL sample 3 with no SNP; lane 5, RL cell line with homozygous SNP. (C) Left hand column: direct sequence of the BAX promoter region. The control sample (I) shows no alteration, whereas a CLL sample (II) shows a heterozygous SNP, and the RL cell line (III) has a homozygous SNP. Middle and right hand columns: corresponding samples digested with the Aci I and Tau I enzymes, respectively

    Techniques Used: Sequencing, Polymerase Chain Reaction, Molecular Weight, Marker, Amplification

    (A) Aci I and (B) Tau I restriction enzyme maps for the BAX promoter region.
    Figure Legend Snippet: (A) Aci I and (B) Tau I restriction enzyme maps for the BAX promoter region.

    Techniques Used:

    Restriction enzyme analysis (with Aci I ) for the G(−248)A single nucleotide polymorphism (SNP) in the BAX gene. M, molecular weight marker (100 bp DNA ladder; Gibco BRL); N, control sample showing three distinct bands, 352 256 bp, and 96 bp; P1, positive control with heterozygous SNP showing the 352 bp (major) and 256 bp (minor) bands and an almost invisible 96 bp band; P2, positive control with a homozygous SNP, which abolishes a restriction enzyme site, resulting in a single 352 bp band; lanes 1–5, chronic lymphocytic leukaemia cases; lanes 1, 4, and 5, heterozygous SNP; lanes 2 and 3, no SNP; lane 6, RL showing the homozygous SNP; lanes 7–12, controls without the G(−248)A SNP.
    Figure Legend Snippet: Restriction enzyme analysis (with Aci I ) for the G(−248)A single nucleotide polymorphism (SNP) in the BAX gene. M, molecular weight marker (100 bp DNA ladder; Gibco BRL); N, control sample showing three distinct bands, 352 256 bp, and 96 bp; P1, positive control with heterozygous SNP showing the 352 bp (major) and 256 bp (minor) bands and an almost invisible 96 bp band; P2, positive control with a homozygous SNP, which abolishes a restriction enzyme site, resulting in a single 352 bp band; lanes 1–5, chronic lymphocytic leukaemia cases; lanes 1, 4, and 5, heterozygous SNP; lanes 2 and 3, no SNP; lane 6, RL showing the homozygous SNP; lanes 7–12, controls without the G(−248)A SNP.

    Techniques Used: Molecular Weight, Marker, Positive Control

    4) Product Images from "Considerations When Analyzing the Methylation Status of PTEN Tumor Suppressor Gene"

    Article Title: Considerations When Analyzing the Methylation Status of PTEN Tumor Suppressor Gene

    Journal: The American Journal of Pathology

    doi:

    Alignment of the PTEN gene ( lower ) and pseudogene ( upper ). The region upstream of nucleotide (−841) represents a divergent sequence. MSP primer sets I, II, and III are shown. Set IV-A, -B primers were used for MSRA to amplify the PTEN gene and pseudogene, respectively. Aci I restriction sites are indicated with triangles. Differences between the two sequences are shown with the pseudogene sequence on top for MSRA are shown. Genomic position is defined by the location relative to the translational start site of PTEN (GenBank accession number AF143312).
    Figure Legend Snippet: Alignment of the PTEN gene ( lower ) and pseudogene ( upper ). The region upstream of nucleotide (−841) represents a divergent sequence. MSP primer sets I, II, and III are shown. Set IV-A, -B primers were used for MSRA to amplify the PTEN gene and pseudogene, respectively. Aci I restriction sites are indicated with triangles. Differences between the two sequences are shown with the pseudogene sequence on top for MSRA are shown. Genomic position is defined by the location relative to the translational start site of PTEN (GenBank accession number AF143312).

    Techniques Used: Sequencing

    Methylation-specific PCR using set III PTEN specific primers ( a ) and methylation-sensitive restriction analysis ( b, c, d ) using primer set IV-A ( PTEN ) respectively for cell lines. MSP analysis, as well as MSRA using primer set IV-A ( PTEN ), show lack of methylation in cell lines ( a, b ). Results for MSRA using set IV-B and -C primers ( c, d ) show methylation positive products in the same cell lines. NL treated with Sss I methyltransferase was used as a methylated positive control. Following Aci I digestion, equal amounts of cell line DNA were used for PCR analysis. U, unmethylated; M, methylated; N, undigested DNA; D, digested DNA; NL, normal lymphocyte DNA.
    Figure Legend Snippet: Methylation-specific PCR using set III PTEN specific primers ( a ) and methylation-sensitive restriction analysis ( b, c, d ) using primer set IV-A ( PTEN ) respectively for cell lines. MSP analysis, as well as MSRA using primer set IV-A ( PTEN ), show lack of methylation in cell lines ( a, b ). Results for MSRA using set IV-B and -C primers ( c, d ) show methylation positive products in the same cell lines. NL treated with Sss I methyltransferase was used as a methylated positive control. Following Aci I digestion, equal amounts of cell line DNA were used for PCR analysis. U, unmethylated; M, methylated; N, undigested DNA; D, digested DNA; NL, normal lymphocyte DNA.

    Techniques Used: Methylation, Polymerase Chain Reaction, Positive Control

    5) Product Images from "APOBEC3G cytosine deamination hotspots are defined by both sequence context and single-stranded DNA secondary structure"

    Article Title: APOBEC3G cytosine deamination hotspots are defined by both sequence context and single-stranded DNA secondary structure

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkt246

    Experimental confirmation of ssDNA secondary structures. Two sets of oligonucleotides with restriction enzyme sites in the stem oligonucleotide were used (( A ) GCCG Set 2 Stem and GCCG Set 2 Open, and ( B ) GCCG Set 1 Stem and GCCG Set 1 Open). The stem bases in the structured oligonucleotides create an Aci I restriction site (A) or a Msp I restriction site (B). The oligonucleotides GCCG Set 2 Open and GCCG Set 1 Open did not fold to form the restriction enzyme sites and remained intact. The average and standard deviation from three independent experiments are shown.
    Figure Legend Snippet: Experimental confirmation of ssDNA secondary structures. Two sets of oligonucleotides with restriction enzyme sites in the stem oligonucleotide were used (( A ) GCCG Set 2 Stem and GCCG Set 2 Open, and ( B ) GCCG Set 1 Stem and GCCG Set 1 Open). The stem bases in the structured oligonucleotides create an Aci I restriction site (A) or a Msp I restriction site (B). The oligonucleotides GCCG Set 2 Open and GCCG Set 1 Open did not fold to form the restriction enzyme sites and remained intact. The average and standard deviation from three independent experiments are shown.

    Techniques Used: Standard Deviation

    6) Product Images from "Detection and Differentiation of Old World Orthopoxviruses: Restriction Fragment Length Polymorphism of the crmB Gene Region"

    Article Title: Detection and Differentiation of Old World Orthopoxviruses: Restriction Fragment Length Polymorphism of the crmB Gene Region

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.39.1.94-100.2001

    RLFP analysis after Aci I digestion of PCR-amplified crmB fragments from genomes of VAR isolates. Lanes: 1, VAR major strain Bangladesh-1975; 2, VAR major strain Congo-1970; 3, VAR major Harvey-1944; 4, African VAR minor Somalia-1977; 5, “Whitepoxch9-2; 6, “Whitepox” ch9-4; 7, alastrim VAR minor strain Sierra Leone-1968; 8, alastrim VAR minor Garcia-1966.
    Figure Legend Snippet: RLFP analysis after Aci I digestion of PCR-amplified crmB fragments from genomes of VAR isolates. Lanes: 1, VAR major strain Bangladesh-1975; 2, VAR major strain Congo-1970; 3, VAR major Harvey-1944; 4, African VAR minor Somalia-1977; 5, “Whitepoxch9-2; 6, “Whitepox” ch9-4; 7, alastrim VAR minor strain Sierra Leone-1968; 8, alastrim VAR minor Garcia-1966.

    Techniques Used: Polymerase Chain Reaction, Amplification

    7) Product Images from "Deconvolution of Nucleic-acid Length Distributions: A Gel Electrophoresis Analysis Tool and Applications"

    Article Title: Deconvolution of Nucleic-acid Length Distributions: A Gel Electrophoresis Analysis Tool and Applications

    Journal: bioRxiv

    doi: 10.1101/636936

    Data used to examine the effect of fragment-density test. (a) The gel was analyzed considering the portions delimited by the ROIs, using lane 1 (blue) as the reference ladder. ROIs 2–6 are tagmentation products of human genomic DNA; 7 and 8 are λ - Aci I digest samples (b) Summary plot of the fit for the gel in (a). Fragment-size mean and standard-deviation values for model distributions containing varying numbers of reference fragments (peaks). Symbols are colored according to the proportion of the original λ - Aci I basis fragments retained in the reference distribution; thus, 1:2 means that every other peak was eliminated from the fit, 2:3 every third peak, etc. Data are also reported in Table S4.
    Figure Legend Snippet: Data used to examine the effect of fragment-density test. (a) The gel was analyzed considering the portions delimited by the ROIs, using lane 1 (blue) as the reference ladder. ROIs 2–6 are tagmentation products of human genomic DNA; 7 and 8 are λ - Aci I digest samples (b) Summary plot of the fit for the gel in (a). Fragment-size mean and standard-deviation values for model distributions containing varying numbers of reference fragments (peaks). Symbols are colored according to the proportion of the original λ - Aci I basis fragments retained in the reference distribution; thus, 1:2 means that every other peak was eliminated from the fit, 2:3 every third peak, etc. Data are also reported in Table S4.

    Techniques Used: Standard Deviation

    Dependence of plug-in output on camera hardware. Estimates of average fragment size obtained for images of the low-resolution gel ( Figure 2c collected using four different camera systems, C1-C4 ( Table 1 ). The plug-in measurements of average fragment size were compared for the known λ - Aci I digest and the same λ -genome tagmented samples analyzed in Figure 2 . Error bars indicate the standard deviation ( i.e ., ) of the fitted distribution. Numerical data for this experiment are also provided in Table S2.
    Figure Legend Snippet: Dependence of plug-in output on camera hardware. Estimates of average fragment size obtained for images of the low-resolution gel ( Figure 2c collected using four different camera systems, C1-C4 ( Table 1 ). The plug-in measurements of average fragment size were compared for the known λ - Aci I digest and the same λ -genome tagmented samples analyzed in Figure 2 . Error bars indicate the standard deviation ( i.e ., ) of the fitted distribution. Numerical data for this experiment are also provided in Table S2.

    Techniques Used: Standard Deviation

    Tagmented libraries prepared from C. elegans genomic DNA. Gel images show the sections corresponding to a low-molecular-weight and b high-molecular-weight fractions. In both cases, lanes 2 and 3 are λ - Aci I digest samples; lanes 4-7 C. elegans genomic-DNA tagmentation reactions amplified by PCR under different conditions. Summary plot of average fragment size based on short- or long-exposure images, c low-molecular-weight, and d high-molecular-weight fractions (Table S3 in table form). Comparison of average fragment sizes obtained using the plug-in to those generated by TapeStation output for the same DNA fractions: e low molecular-weight, and f high molecular-weight (Table S6 in table form).
    Figure Legend Snippet: Tagmented libraries prepared from C. elegans genomic DNA. Gel images show the sections corresponding to a low-molecular-weight and b high-molecular-weight fractions. In both cases, lanes 2 and 3 are λ - Aci I digest samples; lanes 4-7 C. elegans genomic-DNA tagmentation reactions amplified by PCR under different conditions. Summary plot of average fragment size based on short- or long-exposure images, c low-molecular-weight, and d high-molecular-weight fractions (Table S3 in table form). Comparison of average fragment sizes obtained using the plug-in to those generated by TapeStation output for the same DNA fractions: e low molecular-weight, and f high molecular-weight (Table S6 in table form).

    Techniques Used: Molecular Weight, Amplification, Polymerase Chain Reaction, Generated

    8) Product Images from "Hypermethylation of miR-203 in endometrial carcinomas"

    Article Title: Hypermethylation of miR-203 in endometrial carcinomas

    Journal: Gynecologic oncology

    doi: 10.1016/j.ygyno.2014.02.009

    miR-203 is a novel hypermethylated marker in endometrial cancer. (A) The diagram of predicted miRNA binding sites on SOX4 3′-UTR. (B) Summary of the methylation status by COBRA of thirteen miRNA regions in endometrial cancer cell lines (from left to right: AN3CA, Ishikawa, HEC1A, KLE, RL95-2 and SK-UT-1B) and one normal (N) pooled sample derived from two noncancerous endometria as a negative control. m: methylated; and u: unmethylated. (C) Hypermethylation of miR-203 in endometrial cancer cell lines, as revealed by COBRA analysis. E6/E7: normal endometrial cell line; Sss I, methylated positive control; N: normal endometrium. +, Aci I restriction enzyme added; and −, without Aci I.
    Figure Legend Snippet: miR-203 is a novel hypermethylated marker in endometrial cancer. (A) The diagram of predicted miRNA binding sites on SOX4 3′-UTR. (B) Summary of the methylation status by COBRA of thirteen miRNA regions in endometrial cancer cell lines (from left to right: AN3CA, Ishikawa, HEC1A, KLE, RL95-2 and SK-UT-1B) and one normal (N) pooled sample derived from two noncancerous endometria as a negative control. m: methylated; and u: unmethylated. (C) Hypermethylation of miR-203 in endometrial cancer cell lines, as revealed by COBRA analysis. E6/E7: normal endometrial cell line; Sss I, methylated positive control; N: normal endometrium. +, Aci I restriction enzyme added; and −, without Aci I.

    Techniques Used: Marker, Binding Assay, Methylation, Combined Bisulfite Restriction Analysis Assay, Derivative Assay, Negative Control, Positive Control

    9) Product Images from "Modulation of Enhancer Looping and Differential Gene Targeting by Epstein-Barr Virus Transcription Factors Directs Cellular Reprogramming"

    Article Title: Modulation of Enhancer Looping and Differential Gene Targeting by Epstein-Barr Virus Transcription Factors Directs Cellular Reprogramming

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1003636

    The influence of EBNA 3C on chromosome looping at the ADAM28/ADAMDEC1 locus. (A) Diagram (not to scale) showing the Hind III restriction fragments around the ADAM28 locus that encompass the promoter (P), the ADAM enhancer (E, located downstream of ADAM28 ) and two intervening control regions (con1 and con2). The arrow indicates the direction of transcription. (B) Chromosome conformation analysis of the ADAM28 locus in the pz1 control BJAB cell line (−) and the E3C-3 stable EBNA 3C expressing cell line (+) using primer pairs that amplify across promoter-enhancer or promoter-control ligation junctions. Positive controls show PCR amplification from control digestion and ligation reactions carried out using PCR-amplified DNA fragments encompassing the promoter, enhancer and control regions. (C) Diagram (not to scale) showing the Aci I restriction fragments around the ADAMDEC1 locus that encompass the promoter (P), the ADAM enhancer (E, located upstream of ADAMDEC1 ) and an intervening control region (con). The arrow indicates the direction of transcription. (D) Chromosome conformation analysis of the ADAMDEC1 locus in the pz1 control BJAB cell line (−) and the E3C-3 stable EBNA 3C expressing cell line (+) using primer pairs that amplify across promoter-enhancer or promoter-control ligation junctions. Positive controls show PCR amplification from control digestion and ligation reactions carried out using PCR-amplified DNA fragments encompassing the promoter, enhancer and control region.
    Figure Legend Snippet: The influence of EBNA 3C on chromosome looping at the ADAM28/ADAMDEC1 locus. (A) Diagram (not to scale) showing the Hind III restriction fragments around the ADAM28 locus that encompass the promoter (P), the ADAM enhancer (E, located downstream of ADAM28 ) and two intervening control regions (con1 and con2). The arrow indicates the direction of transcription. (B) Chromosome conformation analysis of the ADAM28 locus in the pz1 control BJAB cell line (−) and the E3C-3 stable EBNA 3C expressing cell line (+) using primer pairs that amplify across promoter-enhancer or promoter-control ligation junctions. Positive controls show PCR amplification from control digestion and ligation reactions carried out using PCR-amplified DNA fragments encompassing the promoter, enhancer and control regions. (C) Diagram (not to scale) showing the Aci I restriction fragments around the ADAMDEC1 locus that encompass the promoter (P), the ADAM enhancer (E, located upstream of ADAMDEC1 ) and an intervening control region (con). The arrow indicates the direction of transcription. (D) Chromosome conformation analysis of the ADAMDEC1 locus in the pz1 control BJAB cell line (−) and the E3C-3 stable EBNA 3C expressing cell line (+) using primer pairs that amplify across promoter-enhancer or promoter-control ligation junctions. Positive controls show PCR amplification from control digestion and ligation reactions carried out using PCR-amplified DNA fragments encompassing the promoter, enhancer and control region.

    Techniques Used: Expressing, Ligation, Polymerase Chain Reaction, Amplification

    10) Product Images from "Comparison between single and multi-locus approaches for specimen identification in Mytilus mussels"

    Article Title: Comparison between single and multi-locus approaches for specimen identification in Mytilus mussels

    Journal: Scientific Reports

    doi: 10.1038/s41598-019-55855-8

    Restriction map of markers RFLP-PCR ( a ) Me15-16 Aci I, ( b ) ITS Hha I, ( c ) CO I Xba I and ( d ) 16S rRNA EcoR V, Nhe I and Spe I. *Is used to identify the new haplotypes found in this work. For clarity, we will conserve the name M. galloprovincialis to refer the former Northern Hemisphere haplotype and use M. chilensis for the former Southern Hemisphere haplotype.
    Figure Legend Snippet: Restriction map of markers RFLP-PCR ( a ) Me15-16 Aci I, ( b ) ITS Hha I, ( c ) CO I Xba I and ( d ) 16S rRNA EcoR V, Nhe I and Spe I. *Is used to identify the new haplotypes found in this work. For clarity, we will conserve the name M. galloprovincialis to refer the former Northern Hemisphere haplotype and use M. chilensis for the former Southern Hemisphere haplotype.

    Techniques Used: Polymerase Chain Reaction, Northern Blot

    Heatmaps indicating concordance (% of individuals) in species identification between PCR-RFLP Me15-16 Aci I and each of the other PCR-RFLP markers evaluated ( ITS, CO I and 16S rRNA ) and mac -1.
    Figure Legend Snippet: Heatmaps indicating concordance (% of individuals) in species identification between PCR-RFLP Me15-16 Aci I and each of the other PCR-RFLP markers evaluated ( ITS, CO I and 16S rRNA ) and mac -1.

    Techniques Used: Polymerase Chain Reaction

    Locations and codes for the six sampling sites. Codes for locations can be found in Table S5 . Color indicates species as determined using the PCR-RFLP Me15-16 Aci I assay: red for Mytilus chilensis , orange for Mytilus galloprovincialis , blue for Mytilus edulis and black for Mytilus trossulus . Background topographic map from GeoMapApp ( http://www.geomapapp.org ).
    Figure Legend Snippet: Locations and codes for the six sampling sites. Codes for locations can be found in Table S5 . Color indicates species as determined using the PCR-RFLP Me15-16 Aci I assay: red for Mytilus chilensis , orange for Mytilus galloprovincialis , blue for Mytilus edulis and black for Mytilus trossulus . Background topographic map from GeoMapApp ( http://www.geomapapp.org ).

    Techniques Used: Sampling, Polymerase Chain Reaction

    11) Product Images from "Epigenetic Repression of microRNA-129-2 Leads to Overexpression of SOX4 Oncogene in Endometrial Cancer"

    Article Title: Epigenetic Repression of microRNA-129-2 Leads to Overexpression of SOX4 Oncogene in Endometrial Cancer

    Journal: Cancer research

    doi: 10.1158/0008-5472.CAN-09-1499

    Reactivation of miR-129-2 in cancer cells by pharmacological induction of hyperacetylation and DNA demethylation lead to reduced SOX4 expression at both the mRNA and protein levels. A , genomic map of miR-129-2 CpG island and amplicon. Bar under line, CpG site; ↓, AciI cutting sites. B , COBRA analysis in endometrial cancer cell lines. u, unmethylated band; m, methylated bands; Sss I, 100% methylated control; Blood, a mix of 4 normal peripheral blood samples as negative control; +, Aci I restriction enzyme added; -, without Aci I. C , relative expression levels of miR-129-3p in endometrial cancer cell lines treated with DAC and/or TSA in relation to untreated controls was determined by RT-qPCR analysis. RNU48 was used as internal control gene. Error bar , SD; *, P
    Figure Legend Snippet: Reactivation of miR-129-2 in cancer cells by pharmacological induction of hyperacetylation and DNA demethylation lead to reduced SOX4 expression at both the mRNA and protein levels. A , genomic map of miR-129-2 CpG island and amplicon. Bar under line, CpG site; ↓, AciI cutting sites. B , COBRA analysis in endometrial cancer cell lines. u, unmethylated band; m, methylated bands; Sss I, 100% methylated control; Blood, a mix of 4 normal peripheral blood samples as negative control; +, Aci I restriction enzyme added; -, without Aci I. C , relative expression levels of miR-129-3p in endometrial cancer cell lines treated with DAC and/or TSA in relation to untreated controls was determined by RT-qPCR analysis. RNU48 was used as internal control gene. Error bar , SD; *, P

    Techniques Used: Expressing, Amplification, Combined Bisulfite Restriction Analysis Assay, Methylation, Negative Control, Quantitative RT-PCR

    12) Product Images from "Deconvolution of nucleic-acid length distributions: a gel electrophoresis analysis tool and applications"

    Article Title: Deconvolution of nucleic-acid length distributions: a gel electrophoresis analysis tool and applications

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkz534

    Dependence of plug-in output on camera hardware. Estimates of average fragment size obtained for images of the low-resolution gel (Figure 2C collected using four different camera systems, C1–C4 (Table 1 ). The plug-in measurements of average fragment size were compared for the known λ- Aci I digest and the same λ-genome tagmented samples analyzed in Figure 2 . Error bars indicate the standard deviation (i.e. \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\sqrt{\text{variance}}$\end{document} ) of the fitted distribution. Numerical data for this experiment are also provided in Supplementary Table S2 .
    Figure Legend Snippet: Dependence of plug-in output on camera hardware. Estimates of average fragment size obtained for images of the low-resolution gel (Figure 2C collected using four different camera systems, C1–C4 (Table 1 ). The plug-in measurements of average fragment size were compared for the known λ- Aci I digest and the same λ-genome tagmented samples analyzed in Figure 2 . Error bars indicate the standard deviation (i.e. \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$\sqrt{\text{variance}}$\end{document} ) of the fitted distribution. Numerical data for this experiment are also provided in Supplementary Table S2 .

    Techniques Used: Standard Deviation

    Data used to examine the effect of fragment-density test. ( A ) The gel was analyzed considering the portions delimited by the ROIs, using lane 1 (blue) as the reference ladder. ROIs 2–6 are tagmentation products of human genomic DNA; 7 and 8 are λ- Aci I digest samples ( B ). Summary plot of the fit for the gel in panel (A). Fragment-size mean and standard-deviation values for model distributions containing varying numbers of reference fragments (peaks). Symbols are colored according to the proportion of the original λ- Aci I basis fragments retained in the reference distribution; thus, 1:2 means that every other peak was eliminated from the fit, 2:3 every third peak etc. Data are also reported in Supplementary Table S4 .
    Figure Legend Snippet: Data used to examine the effect of fragment-density test. ( A ) The gel was analyzed considering the portions delimited by the ROIs, using lane 1 (blue) as the reference ladder. ROIs 2–6 are tagmentation products of human genomic DNA; 7 and 8 are λ- Aci I digest samples ( B ). Summary plot of the fit for the gel in panel (A). Fragment-size mean and standard-deviation values for model distributions containing varying numbers of reference fragments (peaks). Symbols are colored according to the proportion of the original λ- Aci I basis fragments retained in the reference distribution; thus, 1:2 means that every other peak was eliminated from the fit, 2:3 every third peak etc. Data are also reported in Supplementary Table S4 .

    Techniques Used: Standard Deviation

    Tagmented libraries prepared from C. elegans genomic DNA. Gel images show the sections corresponding to panel ( A ) low-molecular-weight and panel ( B ) high-molecular-weight fractions. In both cases, lanes 2 and 3 are λ- Aci I digest samples; lanes 4–7 C. elegans genomic-DNA tagmentation reactions amplified by PCR under different conditions. Summary plot of average fragment size based on short- or long-exposure images, panel ( C ) low-molecular-weight and panel ( D ) high-molecular-weight fractions ( Supplementary Table S3 in table form). Comparison of average fragment sizes obtained using the plug-in to those generated by TapeStation output for the same DNA fractions: panel ( E ) low molecular weight and panel ( F ) high molecular weight ( Supplementary Table S6 in table form).
    Figure Legend Snippet: Tagmented libraries prepared from C. elegans genomic DNA. Gel images show the sections corresponding to panel ( A ) low-molecular-weight and panel ( B ) high-molecular-weight fractions. In both cases, lanes 2 and 3 are λ- Aci I digest samples; lanes 4–7 C. elegans genomic-DNA tagmentation reactions amplified by PCR under different conditions. Summary plot of average fragment size based on short- or long-exposure images, panel ( C ) low-molecular-weight and panel ( D ) high-molecular-weight fractions ( Supplementary Table S3 in table form). Comparison of average fragment sizes obtained using the plug-in to those generated by TapeStation output for the same DNA fractions: panel ( E ) low molecular weight and panel ( F ) high molecular weight ( Supplementary Table S6 in table form).

    Techniques Used: Molecular Weight, Amplification, Polymerase Chain Reaction, Generated

    13) Product Images from "Staphylococcus aureus virulence genes identified by bursa aurealis mutagenesis and nematode killing"

    Article Title: Staphylococcus aureus virulence genes identified by bursa aurealis mutagenesis and nematode killing

    Journal: Proceedings of the National Academy of Sciences of the United States of America

    doi: 10.1073/pnas.0404728101

    Plasmids used for transposon mutagenesis in S. aureus . ( A ) Bursa aurealis , a minimariner transposable element, was cloned into pTS2, with a temperature-sensitive plasmid replicon ( rep ts ) and chloramphenicol resistance gene ( cat ) to generate pBursa; the 3.2-kb bursa aurealis encompasses the mariner terminal inverted repeats (TIR), the green fluorescent protein gene ( gfp ), the R6K replication origin ( oriV ), and the erythromycin-resistance determinant ( ermB ). The position of restriction enzyme recognition sites ( Aci I and Bam HI) is indicated. ( B ) Plasmid pFA545 encodes the mariner transposase ( tnp ), the origin of replication ( repC ), and the tetracycline- and ampicillin-resistance markers ( tetBD and bla , respectively). ( C ) The structure of the 5.3-kb transposon Tn 917 with the ermB erythromycin-resistance determinant, tnpR resolvase, and tnpA transposase is shown.
    Figure Legend Snippet: Plasmids used for transposon mutagenesis in S. aureus . ( A ) Bursa aurealis , a minimariner transposable element, was cloned into pTS2, with a temperature-sensitive plasmid replicon ( rep ts ) and chloramphenicol resistance gene ( cat ) to generate pBursa; the 3.2-kb bursa aurealis encompasses the mariner terminal inverted repeats (TIR), the green fluorescent protein gene ( gfp ), the R6K replication origin ( oriV ), and the erythromycin-resistance determinant ( ermB ). The position of restriction enzyme recognition sites ( Aci I and Bam HI) is indicated. ( B ) Plasmid pFA545 encodes the mariner transposase ( tnp ), the origin of replication ( repC ), and the tetracycline- and ampicillin-resistance markers ( tetBD and bla , respectively). ( C ) The structure of the 5.3-kb transposon Tn 917 with the ermB erythromycin-resistance determinant, tnpR resolvase, and tnpA transposase is shown.

    Techniques Used: Mutagenesis, Clone Assay, Plasmid Preparation

    Mapping insertion sites by inverse PCR. Fifteen bursa aurealis transposon mutants of S. aureus strain Newman were subjected to DNA purification, Aci I restriction, fragment ligation, inverse PCR, and agarose gel electrophoresis. M indicates the molecular weight marker (1-kb DNA ladder).
    Figure Legend Snippet: Mapping insertion sites by inverse PCR. Fifteen bursa aurealis transposon mutants of S. aureus strain Newman were subjected to DNA purification, Aci I restriction, fragment ligation, inverse PCR, and agarose gel electrophoresis. M indicates the molecular weight marker (1-kb DNA ladder).

    Techniques Used: Inverse PCR, DNA Purification, Ligation, Agarose Gel Electrophoresis, Molecular Weight, Marker

    Related Articles

    Amplification:

    Article Title: Isolation of Bartonella henselae and Two New Bartonella Subspecies, Bartonellakoehlerae Subspecies boulouisii subsp. nov. and Bartonella koehlerae Subspecies bothieri subsp. nov. from Free-Ranging Californian Mountain Lions and Bobcats
    Article Snippet: .. The amplified product of the gltA gene was digested with Taq I (Promega, Madison, WI), Hha I (New England Biolabs, Beverly, M.A.), Mse I (New England Biolabs) and Aci I (New England Biolabs); the amplified product of the 16S rRNA gene was digested with Dde I (New England Biolabs); the amplified product of the ribC gene was digested with Taq I; and the amplified product of the 16S-23S ITS region was digested with Taq I and Hae III. ..

    Article Title: Comparison of Bacteroides-Prevotella 16S rRNA Genetic Markers for Fecal Samples from Different Animal Species
    Article Snippet: .. Three different restriction digests were performed on each sample by adding 7 μl of amplified product to 5 U of the following restriction enzymes in separate reactions: AciI (New England BioLabs, Beverly MA), HaeIII (Promega, Madison, WI), and MspI (Promega). ..

    Article Title: Modulation of Enhancer Looping and Differential Gene Targeting by Epstein-Barr Virus Transcription Factors Directs Cellular Reprogramming
    Article Snippet: .. As a control for ligation products, genomic DNA regions covering restriction sites of interest were amplified by PCR, purified, mixed in equimolar quantities and then digested with Eco RI-HF, Hind III or Aci I (New England Biolabs) for 1.5 hours. .. Following heat inactivation at 65°C, the digested PCR products were incubated with 10 U T4 DNA-ligase (New England Biolabs) over a temperature range of 4 to 20°C overnight.

    Methylation:

    Article Title: The 2HA line of Medicago truncatula has characteristics of an epigenetic mutant that is weakly ethylene insensitive
    Article Snippet: .. To test for differential methylation within MtEIL1 in 2HA and Jemalong e.g. [ ], DNA (10 μg) was digested overnight by AciI (New England Biolabs, http://www.neb.com ) and cleaned through a PCR clean up column (Promega, http://www.promega.com ). ..

    Ligation:

    Article Title: Modulation of Enhancer Looping and Differential Gene Targeting by Epstein-Barr Virus Transcription Factors Directs Cellular Reprogramming
    Article Snippet: .. As a control for ligation products, genomic DNA regions covering restriction sites of interest were amplified by PCR, purified, mixed in equimolar quantities and then digested with Eco RI-HF, Hind III or Aci I (New England Biolabs) for 1.5 hours. .. Following heat inactivation at 65°C, the digested PCR products were incubated with 10 U T4 DNA-ligase (New England Biolabs) over a temperature range of 4 to 20°C overnight.

    Purification:

    Article Title: Modulation of Enhancer Looping and Differential Gene Targeting by Epstein-Barr Virus Transcription Factors Directs Cellular Reprogramming
    Article Snippet: .. As a control for ligation products, genomic DNA regions covering restriction sites of interest were amplified by PCR, purified, mixed in equimolar quantities and then digested with Eco RI-HF, Hind III or Aci I (New England Biolabs) for 1.5 hours. .. Following heat inactivation at 65°C, the digested PCR products were incubated with 10 U T4 DNA-ligase (New England Biolabs) over a temperature range of 4 to 20°C overnight.

    Incubation:

    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 Aci I (New England Biolabs) at 37°C for 16 hours. .. Aci I digests only unmethylated DNA at its recognition sequence (5′- C↓ CGC- 3′), leaving methylated sites intact.

    Activity Assay:

    Article Title: Epstein-Barr Virus Rta-Mediated Accumulation of DNA Methylation Interferes with CTCF Binding in both Host and Viral Genomes
    Article Snippet: .. For each sample, 5 μg DNA was digested by AciI, HpaII, and HinP1I (NEB Inc.) at 37°C for 30 min, followed by heat inactivation to eliminate enzyme activity. .. EcoRI (NEB Inc.), which is insensitive to CpG methylation, was run in parallel to serve as a DNA input control.

    Polymerase Chain Reaction:

    Article Title: The 2HA line of Medicago truncatula has characteristics of an epigenetic mutant that is weakly ethylene insensitive
    Article Snippet: .. To test for differential methylation within MtEIL1 in 2HA and Jemalong e.g. [ ], DNA (10 μg) was digested overnight by AciI (New England Biolabs, http://www.neb.com ) and cleaned through a PCR clean up column (Promega, http://www.promega.com ). ..

    Article Title: Modulation of Enhancer Looping and Differential Gene Targeting by Epstein-Barr Virus Transcription Factors Directs Cellular Reprogramming
    Article Snippet: .. As a control for ligation products, genomic DNA regions covering restriction sites of interest were amplified by PCR, purified, mixed in equimolar quantities and then digested with Eco RI-HF, Hind III or Aci I (New England Biolabs) for 1.5 hours. .. Following heat inactivation at 65°C, the digested PCR products were incubated with 10 U T4 DNA-ligase (New England Biolabs) over a temperature range of 4 to 20°C overnight.

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    New England Biolabs aci i
    PCR-RFLP of a gltA gene fragment using the restriction endonuclease <t>Aci</t> I. Lanes 1, 4 and 19 show 100 BP Ladder; Lane 2, Mt Lion L27-96; Lane 3, Mt Lion L42-94; Lane 5, Mt Lion L-39-97; Lane 6, Mt Lion FM98061; Lane 7, Bobcat L08-96; Lane 8, Bobcat L17-96; Lane 9, Bobcat DS08; Lane 10, Bobcat L10-97; Lane 11, Bobcat L11-97; Lane 12, Bobcat SC443; lane 13, Bobcat DS507; Lane 14, B . henselae Type I; Lane 15, B . henselae Type II; Lane 16, B . clarridgeiae ; Lane 17, B . koehlerae ; Lane18, B . bovis (“weissii” isolate).
    Aci I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 34 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/aci i/product/New England Biolabs
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    aci i - by Bioz Stars, 2020-09
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    85
    New England Biolabs restriction enzyme aci i
    Map of transposon bursa aurealis and plasmids used for delivery along with summary of steps involved in the mapping of insertion sites by inverse PCR. (A) Bursa aurealis (3.2 kbp), a mini-mariner transposable element, was cloned into pTS2, with a temperature-sensitive plasmid replicon (rep ts ) and chloramphenicol resistance gene cat to generate pBursa (7,383 bp). Bursa aurealis encompasses mariner terminal inverted repeats (TIR), R6K replication origin (oriV) for replication in E. coli , and erythromycin-resistance determinant ermC , an rRNA methylase that allows selection in both E. coli and S. aureus . The position of the most terminal site for the restriction enzyme <t>Aci</t> I is indicated as well as the site of hybridization and nucleotide sequence of primer Martn-F (F). Plasmid pFA545 (10,079 bp) encodes the mariner transposase tnp and is a derivative of pSPT181, a shuttle vector consisting of pSP64 with ampicillin resistance ( bla ) for replication and selection in E. coli , and pRN8103, a temperature-sensitive derivative of pT181 (rep ts ) and tetracycline-resistance marker ( tetB tetD ). The presence of rep ts and tetBD allows for replication of pFA545 in S. aureus and other Gram-positive bacteria. (B) Mapping insertion sites by inverse PCR. Genome DNA from a candidate mutant strain is isolated and digested with Aci I. Next, fragment self-ligation and inverse PCR are performed using DNA ligase and primers Martn-F (F) and Martn-ermR (R). PCR products are subjected to DNA sequence analysis using primer Martn-F (F).
    Restriction Enzyme Aci I, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 85/100, based on 4 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/restriction enzyme aci i/product/New England Biolabs
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    Image Search Results


    PCR-RFLP of a gltA gene fragment using the restriction endonuclease Aci I. Lanes 1, 4 and 19 show 100 BP Ladder; Lane 2, Mt Lion L27-96; Lane 3, Mt Lion L42-94; Lane 5, Mt Lion L-39-97; Lane 6, Mt Lion FM98061; Lane 7, Bobcat L08-96; Lane 8, Bobcat L17-96; Lane 9, Bobcat DS08; Lane 10, Bobcat L10-97; Lane 11, Bobcat L11-97; Lane 12, Bobcat SC443; lane 13, Bobcat DS507; Lane 14, B . henselae Type I; Lane 15, B . henselae Type II; Lane 16, B . clarridgeiae ; Lane 17, B . koehlerae ; Lane18, B . bovis (“weissii” isolate).

    Journal: PLoS ONE

    Article Title: Isolation of Bartonella henselae and Two New Bartonella Subspecies, Bartonellakoehlerae Subspecies boulouisii subsp. nov. and Bartonella koehlerae Subspecies bothieri subsp. nov. from Free-Ranging Californian Mountain Lions and Bobcats

    doi: 10.1371/journal.pone.0148299

    Figure Lengend Snippet: PCR-RFLP of a gltA gene fragment using the restriction endonuclease Aci I. Lanes 1, 4 and 19 show 100 BP Ladder; Lane 2, Mt Lion L27-96; Lane 3, Mt Lion L42-94; Lane 5, Mt Lion L-39-97; Lane 6, Mt Lion FM98061; Lane 7, Bobcat L08-96; Lane 8, Bobcat L17-96; Lane 9, Bobcat DS08; Lane 10, Bobcat L10-97; Lane 11, Bobcat L11-97; Lane 12, Bobcat SC443; lane 13, Bobcat DS507; Lane 14, B . henselae Type I; Lane 15, B . henselae Type II; Lane 16, B . clarridgeiae ; Lane 17, B . koehlerae ; Lane18, B . bovis (“weissii” isolate).

    Article Snippet: The amplified product of the gltA gene was digested with Taq I (Promega, Madison, WI), Hha I (New England Biolabs, Beverly, M.A.), Mse I (New England Biolabs) and Aci I (New England Biolabs); the amplified product of the 16S rRNA gene was digested with Dde I (New England Biolabs); the amplified product of the ribC gene was digested with Taq I; and the amplified product of the 16S-23S ITS region was digested with Taq I and Hae III.

    Techniques: Polymerase Chain Reaction

    The influence of EBNA 3C on chromosome looping at the ADAM28/ADAMDEC1 locus. (A) Diagram (not to scale) showing the Hind III restriction fragments around the ADAM28 locus that encompass the promoter (P), the ADAM enhancer (E, located downstream of ADAM28 ) and two intervening control regions (con1 and con2). The arrow indicates the direction of transcription. (B) Chromosome conformation analysis of the ADAM28 locus in the pz1 control BJAB cell line (−) and the E3C-3 stable EBNA 3C expressing cell line (+) using primer pairs that amplify across promoter-enhancer or promoter-control ligation junctions. Positive controls show PCR amplification from control digestion and ligation reactions carried out using PCR-amplified DNA fragments encompassing the promoter, enhancer and control regions. (C) Diagram (not to scale) showing the Aci I restriction fragments around the ADAMDEC1 locus that encompass the promoter (P), the ADAM enhancer (E, located upstream of ADAMDEC1 ) and an intervening control region (con). The arrow indicates the direction of transcription. (D) Chromosome conformation analysis of the ADAMDEC1 locus in the pz1 control BJAB cell line (−) and the E3C-3 stable EBNA 3C expressing cell line (+) using primer pairs that amplify across promoter-enhancer or promoter-control ligation junctions. Positive controls show PCR amplification from control digestion and ligation reactions carried out using PCR-amplified DNA fragments encompassing the promoter, enhancer and control region.

    Journal: PLoS Pathogens

    Article Title: Modulation of Enhancer Looping and Differential Gene Targeting by Epstein-Barr Virus Transcription Factors Directs Cellular Reprogramming

    doi: 10.1371/journal.ppat.1003636

    Figure Lengend Snippet: The influence of EBNA 3C on chromosome looping at the ADAM28/ADAMDEC1 locus. (A) Diagram (not to scale) showing the Hind III restriction fragments around the ADAM28 locus that encompass the promoter (P), the ADAM enhancer (E, located downstream of ADAM28 ) and two intervening control regions (con1 and con2). The arrow indicates the direction of transcription. (B) Chromosome conformation analysis of the ADAM28 locus in the pz1 control BJAB cell line (−) and the E3C-3 stable EBNA 3C expressing cell line (+) using primer pairs that amplify across promoter-enhancer or promoter-control ligation junctions. Positive controls show PCR amplification from control digestion and ligation reactions carried out using PCR-amplified DNA fragments encompassing the promoter, enhancer and control regions. (C) Diagram (not to scale) showing the Aci I restriction fragments around the ADAMDEC1 locus that encompass the promoter (P), the ADAM enhancer (E, located upstream of ADAMDEC1 ) and an intervening control region (con). The arrow indicates the direction of transcription. (D) Chromosome conformation analysis of the ADAMDEC1 locus in the pz1 control BJAB cell line (−) and the E3C-3 stable EBNA 3C expressing cell line (+) using primer pairs that amplify across promoter-enhancer or promoter-control ligation junctions. Positive controls show PCR amplification from control digestion and ligation reactions carried out using PCR-amplified DNA fragments encompassing the promoter, enhancer and control region.

    Article Snippet: As a control for ligation products, genomic DNA regions covering restriction sites of interest were amplified by PCR, purified, mixed in equimolar quantities and then digested with Eco RI-HF, Hind III or Aci I (New England Biolabs) for 1.5 hours.

    Techniques: Expressing, Ligation, Polymerase Chain Reaction, Amplification

    Restriction enzyme analysis and parallel direct sequencing of polymerase chain reaction (PCR) products. (A) Aci I and (B) Tau I endonuclease cleavage followed by 10% polyacrylamide gel analysis. M, molecular weight marker, 100 bp DNA ladder (Gibco BRL, Burlington, Ontario, Canada). (A) Lane 1, chronic lymphocytic leukaemia (CLL) sample 1, amplified BAX promoter segment before digestion; lanes 2–5, PCR products digested with Aci I; lane 2, CLL sample 2 with a heterozygous single nucleotide polymorphism (SNP); lanes 3 and 4, CLL samples 3 and 4 with no SNP; lane 5, RL cell line with homozygous SNP. (B) PCR products digested with Tau I; lane 2, CLL sample 2 with a heterozygous SNP; lane 3, CLL sample 3 with no SNP; lane 5, RL cell line with homozygous SNP. (C) Left hand column: direct sequence of the BAX promoter region. The control sample (I) shows no alteration, whereas a CLL sample (II) shows a heterozygous SNP, and the RL cell line (III) has a homozygous SNP. Middle and right hand columns: corresponding samples digested with the Aci I and Tau I enzymes, respectively

    Journal: Molecular Pathology

    Article Title: Molecular detection of the G(-248)A BAX promoter nucleotide change in B cell chronic lymphocytic leukaemia

    doi:

    Figure Lengend Snippet: Restriction enzyme analysis and parallel direct sequencing of polymerase chain reaction (PCR) products. (A) Aci I and (B) Tau I endonuclease cleavage followed by 10% polyacrylamide gel analysis. M, molecular weight marker, 100 bp DNA ladder (Gibco BRL, Burlington, Ontario, Canada). (A) Lane 1, chronic lymphocytic leukaemia (CLL) sample 1, amplified BAX promoter segment before digestion; lanes 2–5, PCR products digested with Aci I; lane 2, CLL sample 2 with a heterozygous single nucleotide polymorphism (SNP); lanes 3 and 4, CLL samples 3 and 4 with no SNP; lane 5, RL cell line with homozygous SNP. (B) PCR products digested with Tau I; lane 2, CLL sample 2 with a heterozygous SNP; lane 3, CLL sample 3 with no SNP; lane 5, RL cell line with homozygous SNP. (C) Left hand column: direct sequence of the BAX promoter region. The control sample (I) shows no alteration, whereas a CLL sample (II) shows a heterozygous SNP, and the RL cell line (III) has a homozygous SNP. Middle and right hand columns: corresponding samples digested with the Aci I and Tau I enzymes, respectively

    Article Snippet: Two restriction enzymes, Aci I (New England BioLabs Inc, Mississauga, Ontario, Canada) and Tau I (MBI Fermentas, Burlington, Ontario, Canada) were used to screen the samples for the SNP detection (fig 1 ).

    Techniques: Sequencing, Polymerase Chain Reaction, Molecular Weight, Marker, Amplification

    (A) Aci I and (B) Tau I restriction enzyme maps for the BAX promoter region.

    Journal: Molecular Pathology

    Article Title: Molecular detection of the G(-248)A BAX promoter nucleotide change in B cell chronic lymphocytic leukaemia

    doi:

    Figure Lengend Snippet: (A) Aci I and (B) Tau I restriction enzyme maps for the BAX promoter region.

    Article Snippet: Two restriction enzymes, Aci I (New England BioLabs Inc, Mississauga, Ontario, Canada) and Tau I (MBI Fermentas, Burlington, Ontario, Canada) were used to screen the samples for the SNP detection (fig 1 ).

    Techniques:

    Restriction enzyme analysis (with Aci I ) for the G(−248)A single nucleotide polymorphism (SNP) in the BAX gene. M, molecular weight marker (100 bp DNA ladder; Gibco BRL); N, control sample showing three distinct bands, 352 256 bp, and 96 bp; P1, positive control with heterozygous SNP showing the 352 bp (major) and 256 bp (minor) bands and an almost invisible 96 bp band; P2, positive control with a homozygous SNP, which abolishes a restriction enzyme site, resulting in a single 352 bp band; lanes 1–5, chronic lymphocytic leukaemia cases; lanes 1, 4, and 5, heterozygous SNP; lanes 2 and 3, no SNP; lane 6, RL showing the homozygous SNP; lanes 7–12, controls without the G(−248)A SNP.

    Journal: Molecular Pathology

    Article Title: Molecular detection of the G(-248)A BAX promoter nucleotide change in B cell chronic lymphocytic leukaemia

    doi:

    Figure Lengend Snippet: Restriction enzyme analysis (with Aci I ) for the G(−248)A single nucleotide polymorphism (SNP) in the BAX gene. M, molecular weight marker (100 bp DNA ladder; Gibco BRL); N, control sample showing three distinct bands, 352 256 bp, and 96 bp; P1, positive control with heterozygous SNP showing the 352 bp (major) and 256 bp (minor) bands and an almost invisible 96 bp band; P2, positive control with a homozygous SNP, which abolishes a restriction enzyme site, resulting in a single 352 bp band; lanes 1–5, chronic lymphocytic leukaemia cases; lanes 1, 4, and 5, heterozygous SNP; lanes 2 and 3, no SNP; lane 6, RL showing the homozygous SNP; lanes 7–12, controls without the G(−248)A SNP.

    Article Snippet: Two restriction enzymes, Aci I (New England BioLabs Inc, Mississauga, Ontario, Canada) and Tau I (MBI Fermentas, Burlington, Ontario, Canada) were used to screen the samples for the SNP detection (fig 1 ).

    Techniques: Molecular Weight, Marker, Positive Control

    Map of transposon bursa aurealis and plasmids used for delivery along with summary of steps involved in the mapping of insertion sites by inverse PCR. (A) Bursa aurealis (3.2 kbp), a mini-mariner transposable element, was cloned into pTS2, with a temperature-sensitive plasmid replicon (rep ts ) and chloramphenicol resistance gene cat to generate pBursa (7,383 bp). Bursa aurealis encompasses mariner terminal inverted repeats (TIR), R6K replication origin (oriV) for replication in E. coli , and erythromycin-resistance determinant ermC , an rRNA methylase that allows selection in both E. coli and S. aureus . The position of the most terminal site for the restriction enzyme Aci I is indicated as well as the site of hybridization and nucleotide sequence of primer Martn-F (F). Plasmid pFA545 (10,079 bp) encodes the mariner transposase tnp and is a derivative of pSPT181, a shuttle vector consisting of pSP64 with ampicillin resistance ( bla ) for replication and selection in E. coli , and pRN8103, a temperature-sensitive derivative of pT181 (rep ts ) and tetracycline-resistance marker ( tetB tetD ). The presence of rep ts and tetBD allows for replication of pFA545 in S. aureus and other Gram-positive bacteria. (B) Mapping insertion sites by inverse PCR. Genome DNA from a candidate mutant strain is isolated and digested with Aci I. Next, fragment self-ligation and inverse PCR are performed using DNA ligase and primers Martn-F (F) and Martn-ermR (R). PCR products are subjected to DNA sequence analysis using primer Martn-F (F).

    Journal: Current protocols in microbiology

    Article Title: Genetic manipulation of Staphylococcus aureus

    doi: 10.1002/9780471729259.mc09c03s32

    Figure Lengend Snippet: Map of transposon bursa aurealis and plasmids used for delivery along with summary of steps involved in the mapping of insertion sites by inverse PCR. (A) Bursa aurealis (3.2 kbp), a mini-mariner transposable element, was cloned into pTS2, with a temperature-sensitive plasmid replicon (rep ts ) and chloramphenicol resistance gene cat to generate pBursa (7,383 bp). Bursa aurealis encompasses mariner terminal inverted repeats (TIR), R6K replication origin (oriV) for replication in E. coli , and erythromycin-resistance determinant ermC , an rRNA methylase that allows selection in both E. coli and S. aureus . The position of the most terminal site for the restriction enzyme Aci I is indicated as well as the site of hybridization and nucleotide sequence of primer Martn-F (F). Plasmid pFA545 (10,079 bp) encodes the mariner transposase tnp and is a derivative of pSPT181, a shuttle vector consisting of pSP64 with ampicillin resistance ( bla ) for replication and selection in E. coli , and pRN8103, a temperature-sensitive derivative of pT181 (rep ts ) and tetracycline-resistance marker ( tetB tetD ). The presence of rep ts and tetBD allows for replication of pFA545 in S. aureus and other Gram-positive bacteria. (B) Mapping insertion sites by inverse PCR. Genome DNA from a candidate mutant strain is isolated and digested with Aci I. Next, fragment self-ligation and inverse PCR are performed using DNA ligase and primers Martn-F (F) and Martn-ermR (R). PCR products are subjected to DNA sequence analysis using primer Martn-F (F).

    Article Snippet: Restriction enzyme Aci I, T4 DNA ligase, polymerase for PCR amplification (New England Biolabs or preferred commercial source) 37°C incubator Eppendorf and PCR tubes, tips and pipetman Qiagen MinElute 96 UF PCR purification Kit (or preferred kit for purification of DNA fragments) PCR machine 1.

    Techniques: Inverse PCR, Clone Assay, Plasmid Preparation, Selection, Hybridization, Sequencing, Marker, Mutagenesis, Isolation, Ligation, Polymerase Chain Reaction