bal31 nuclease  (New England Biolabs)


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  • 99
    Name:
    Nuclease BAL 31
    Description:
    Nuclease BAL 31 50 units
    Catalog Number:
    m0213s
    Price:
    68
    Size:
    50 units
    Category:
    Exonucleases
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    Structured Review

    New England Biolabs bal31 nuclease
    Nuclease BAL 31
    Nuclease BAL 31 50 units
    https://www.bioz.com/result/bal31 nuclease/product/New England Biolabs
    Average 99 stars, based on 3 article reviews
    Price from $9.99 to $1999.99
    bal31 nuclease - by Bioz Stars, 2020-04
    99/100 stars

    Images

    1) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    2) Product Images from "Cooperative kinking at distant sites in mechanically stressed DNA"

    Article Title: Cooperative kinking at distant sites in mechanically stressed DNA

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkr666

    DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.
    Figure Legend Snippet: DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.

    Techniques Used: Polyacrylamide Gel Electrophoresis, Marker

    3) Product Images from "Production of DNA minicircles less than 250 base pairs through a novel concentrated DNA circularization assay enabling minicircle design with NF-κB inhibition activity"

    Article Title: Production of DNA minicircles less than 250 base pairs through a novel concentrated DNA circularization assay enabling minicircle design with NF-κB inhibition activity

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkw1034

    CNDCA-based production of supercoiled minicircle. Image of stained native polyacrylamide gel showing 95 bp minicircle topoisomers of decreased linking number (ΔLk values of −1 and −2) (lanes 4, 6) as indicated on the right and obtained by religation of the nicked minicircle in the presence of EtBr. The slowest migrating band corresponds to the relaxed minicircle that migrates expectedly at the same rate as the nicked minicircle (lanes 1 and 2). Digestion of minicircle samples by the nuclease Bal31 is indicated on the right. The position of the molecular mass markers in bp is indicated on the left.
    Figure Legend Snippet: CNDCA-based production of supercoiled minicircle. Image of stained native polyacrylamide gel showing 95 bp minicircle topoisomers of decreased linking number (ΔLk values of −1 and −2) (lanes 4, 6) as indicated on the right and obtained by religation of the nicked minicircle in the presence of EtBr. The slowest migrating band corresponds to the relaxed minicircle that migrates expectedly at the same rate as the nicked minicircle (lanes 1 and 2). Digestion of minicircle samples by the nuclease Bal31 is indicated on the right. The position of the molecular mass markers in bp is indicated on the left.

    Techniques Used: Staining

    4) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    5) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    6) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    7) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    8) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    9) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    10) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    11) Product Images from "Cooperative kinking at distant sites in mechanically stressed DNA"

    Article Title: Cooperative kinking at distant sites in mechanically stressed DNA

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkr666

    DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.
    Figure Legend Snippet: DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.

    Techniques Used: Polyacrylamide Gel Electrophoresis, Marker

    12) Product Images from "Production of DNA minicircles less than 250 base pairs through a novel concentrated DNA circularization assay enabling minicircle design with NF-κB inhibition activity"

    Article Title: Production of DNA minicircles less than 250 base pairs through a novel concentrated DNA circularization assay enabling minicircle design with NF-κB inhibition activity

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkw1034

    CNDCA-based production of supercoiled minicircle. Image of stained native polyacrylamide gel showing 95 bp minicircle topoisomers of decreased linking number (ΔLk values of −1 and −2) (lanes 4, 6) as indicated on the right and obtained by religation of the nicked minicircle in the presence of EtBr. The slowest migrating band corresponds to the relaxed minicircle that migrates expectedly at the same rate as the nicked minicircle (lanes 1 and 2). Digestion of minicircle samples by the nuclease Bal31 is indicated on the right. The position of the molecular mass markers in bp is indicated on the left.
    Figure Legend Snippet: CNDCA-based production of supercoiled minicircle. Image of stained native polyacrylamide gel showing 95 bp minicircle topoisomers of decreased linking number (ΔLk values of −1 and −2) (lanes 4, 6) as indicated on the right and obtained by religation of the nicked minicircle in the presence of EtBr. The slowest migrating band corresponds to the relaxed minicircle that migrates expectedly at the same rate as the nicked minicircle (lanes 1 and 2). Digestion of minicircle samples by the nuclease Bal31 is indicated on the right. The position of the molecular mass markers in bp is indicated on the left.

    Techniques Used: Staining

    13) Product Images from "Novel Virulent and Broad-Host-Range Erwinia amylovora Bacteriophages Reveal a High Degree of Mosaicism and a Relationship to Enterobacteriaceae Phages ▿ Phages ▿ †"

    Article Title: Novel Virulent and Broad-Host-Range Erwinia amylovora Bacteriophages Reveal a High Degree of Mosaicism and a Relationship to Enterobacteriaceae Phages ▿ Phages ▿ †

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.03022-10

    Analysis of phage genome physical structures. Shown are fragment patterns of phage DNA, following time-limited BAL31 treatment and subsequent digestion with different endonucleases. Phage L1 was digested with MfeI, M7 with FspBI, S6 with three different
    Figure Legend Snippet: Analysis of phage genome physical structures. Shown are fragment patterns of phage DNA, following time-limited BAL31 treatment and subsequent digestion with different endonucleases. Phage L1 was digested with MfeI, M7 with FspBI, S6 with three different

    Techniques Used:

    14) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    15) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    16) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    17) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    18) Product Images from "Cooperative kinking at distant sites in mechanically stressed DNA"

    Article Title: Cooperative kinking at distant sites in mechanically stressed DNA

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkr666

    DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.
    Figure Legend Snippet: DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.

    Techniques Used: Polyacrylamide Gel Electrophoresis, Marker

    19) Product Images from "Cooperative kinking at distant sites in mechanically stressed DNA"

    Article Title: Cooperative kinking at distant sites in mechanically stressed DNA

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkr666

    DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.
    Figure Legend Snippet: DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.

    Techniques Used: Polyacrylamide Gel Electrophoresis, Marker

    20) Product Images from "Chromatin features of plant telomeric sequences at terminal vs. internal positions"

    Article Title: Chromatin features of plant telomeric sequences at terminal vs. internal positions

    Journal: Frontiers in Plant Science

    doi: 10.3389/fpls.2014.00593

    Internal localization of telomeric repeats in the B. antipoda genome. (A) High molecular weight DNA digested by Bal31 nuclease and a mix of frequently cutting restriction enzymes was analyzed by pulse field gel electrophoresis. Signals after hybridization with the radioactively labeled telomeric oligonucleotide showed resistance of telomeric sequences to Bal31 cleavage. The apparent decrease in signal intensity after 30 min of Bal31 digestion reflects variation in sample loading rather than a change due to the Bal31 treatment (compare to the signal after 45 min of Bal31). (B) DNA released into solution in the course of Bal31 digestions was purified and subjected to conventional agarose electrophoresis. The numbers above lines indicate the time of Bal31 digestion in minutes. M, DNA size markers.
    Figure Legend Snippet: Internal localization of telomeric repeats in the B. antipoda genome. (A) High molecular weight DNA digested by Bal31 nuclease and a mix of frequently cutting restriction enzymes was analyzed by pulse field gel electrophoresis. Signals after hybridization with the radioactively labeled telomeric oligonucleotide showed resistance of telomeric sequences to Bal31 cleavage. The apparent decrease in signal intensity after 30 min of Bal31 digestion reflects variation in sample loading rather than a change due to the Bal31 treatment (compare to the signal after 45 min of Bal31). (B) DNA released into solution in the course of Bal31 digestions was purified and subjected to conventional agarose electrophoresis. The numbers above lines indicate the time of Bal31 digestion in minutes. M, DNA size markers.

    Techniques Used: Molecular Weight, Nucleic Acid Electrophoresis, Hybridization, Labeling, Purification, Electrophoresis

    Relative cytosine methylation in telomeres of Nicotiana species. (A) After Bal31 treatment of N. tabacum high molecular weight DNA, TRF analysis was used to control the efficiency of digestion. A loss of the telomere-specific hybridization signal was observed in the course of Bal31 treatment. After 15 min of Bal31 digestion loss of the signal is evident but telomere erosion is not clear, whereas after 45- and 90-min treatments, telomeres were efficiently degraded. Time of Bal31 digestion is given above the lanes. M – DNA size marker. (B) Dot-blot analysis of Bal31-digested DNA from N. tabacum and N. tomentosiformis after treatment with sodium bisulfite. Samples were loaded onto a membrane and hybridized with radioactively labeled probes to detect the total signal of telomeres (loading probe pltel-C complementary to the telomeric G-strand) and the portion of methylated telomeres (DEGENER probe). Time of the Bal31 digestion in minutes is given above the membranes. +, positive hybridization control (tobacco DNA without the bisulfite treatment); −, negative control (DNA from the pUC19 plasmid). (C) Relative density of methylated cytosines along telomeres, calculated as the DEGENER/loading hybridization signals ratio. The ratio in Bal31 non-treated samples was arbitrarily taken as 1. Six independent experiments were performed.
    Figure Legend Snippet: Relative cytosine methylation in telomeres of Nicotiana species. (A) After Bal31 treatment of N. tabacum high molecular weight DNA, TRF analysis was used to control the efficiency of digestion. A loss of the telomere-specific hybridization signal was observed in the course of Bal31 treatment. After 15 min of Bal31 digestion loss of the signal is evident but telomere erosion is not clear, whereas after 45- and 90-min treatments, telomeres were efficiently degraded. Time of Bal31 digestion is given above the lanes. M – DNA size marker. (B) Dot-blot analysis of Bal31-digested DNA from N. tabacum and N. tomentosiformis after treatment with sodium bisulfite. Samples were loaded onto a membrane and hybridized with radioactively labeled probes to detect the total signal of telomeres (loading probe pltel-C complementary to the telomeric G-strand) and the portion of methylated telomeres (DEGENER probe). Time of the Bal31 digestion in minutes is given above the membranes. +, positive hybridization control (tobacco DNA without the bisulfite treatment); −, negative control (DNA from the pUC19 plasmid). (C) Relative density of methylated cytosines along telomeres, calculated as the DEGENER/loading hybridization signals ratio. The ratio in Bal31 non-treated samples was arbitrarily taken as 1. Six independent experiments were performed.

    Techniques Used: Methylation, Molecular Weight, Hybridization, Marker, Dot Blot, Labeling, Negative Control, Plasmid Preparation

    Methylation of cytosines of B. antipoda telomeric repeats. (A) Analysis of global methylation of cytosines in telomeric repeats of B. antipoda . High molecular weight DNA was treated with Bal31, converted with bisulfite and analyzed by Southern hybridization against loading and DEGENER probes. Signals with the DEGENER probe indicating methylated cytosines in telomeric repeats were obtained in all samples. The time of Bal31 digestion is given above the membranes. +, positive hybridization control (tobacco DNA without the bisulfite treatment); −, negative control (DNA from pUC19 plasmid). (B) An example of bisulfite sequencing data for Ba493 and Ba576 regions in adult leaves. Non-symmetrically located cytosines are depicted as green triangles; full triangle, methylated; empty triangle, non-methylated cytosine. Cytosines located in perfect telomeric repeats are underlined. The first line of the scheme where all cytosines in all sequence contexts are presented as full figures represents position of respective cytosine. (C) Graphical representation of telomeric cytosine methylation within the ITR-containing sequences Ba493 and Ba576. Three tissues were analyzed to reveal possible tissue-specific methylation pattern. “all,” all cytosines located in non-symmetrical sequence context; “telomeric,” cytosines located in perfect telomeric repeats. Data were processed by One-Way independent ANOVA test with standard weighted-means, * is used for P
    Figure Legend Snippet: Methylation of cytosines of B. antipoda telomeric repeats. (A) Analysis of global methylation of cytosines in telomeric repeats of B. antipoda . High molecular weight DNA was treated with Bal31, converted with bisulfite and analyzed by Southern hybridization against loading and DEGENER probes. Signals with the DEGENER probe indicating methylated cytosines in telomeric repeats were obtained in all samples. The time of Bal31 digestion is given above the membranes. +, positive hybridization control (tobacco DNA without the bisulfite treatment); −, negative control (DNA from pUC19 plasmid). (B) An example of bisulfite sequencing data for Ba493 and Ba576 regions in adult leaves. Non-symmetrically located cytosines are depicted as green triangles; full triangle, methylated; empty triangle, non-methylated cytosine. Cytosines located in perfect telomeric repeats are underlined. The first line of the scheme where all cytosines in all sequence contexts are presented as full figures represents position of respective cytosine. (C) Graphical representation of telomeric cytosine methylation within the ITR-containing sequences Ba493 and Ba576. Three tissues were analyzed to reveal possible tissue-specific methylation pattern. “all,” all cytosines located in non-symmetrical sequence context; “telomeric,” cytosines located in perfect telomeric repeats. Data were processed by One-Way independent ANOVA test with standard weighted-means, * is used for P

    Techniques Used: Methylation, Molecular Weight, Hybridization, Negative Control, Plasmid Preparation, Methylation Sequencing, Sequencing

    21) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    22) Product Images from "Novel Virulent and Broad-Host-Range Erwinia amylovora Bacteriophages Reveal a High Degree of Mosaicism and a Relationship to Enterobacteriaceae Phages ▿ Phages ▿ †"

    Article Title: Novel Virulent and Broad-Host-Range Erwinia amylovora Bacteriophages Reveal a High Degree of Mosaicism and a Relationship to Enterobacteriaceae Phages ▿ Phages ▿ †

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.03022-10

    Analysis of phage genome physical structures. Shown are fragment patterns of phage DNA, following time-limited BAL31 treatment and subsequent digestion with different endonucleases. Phage L1 was digested with MfeI, M7 with FspBI, S6 with three different
    Figure Legend Snippet: Analysis of phage genome physical structures. Shown are fragment patterns of phage DNA, following time-limited BAL31 treatment and subsequent digestion with different endonucleases. Phage L1 was digested with MfeI, M7 with FspBI, S6 with three different

    Techniques Used:

    23) Product Images from "Cooperative kinking at distant sites in mechanically stressed DNA"

    Article Title: Cooperative kinking at distant sites in mechanically stressed DNA

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkr666

    DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.
    Figure Legend Snippet: DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.

    Techniques Used: Polyacrylamide Gel Electrophoresis, Marker

    24) Product Images from "Cooperative kinking at distant sites in mechanically stressed DNA"

    Article Title: Cooperative kinking at distant sites in mechanically stressed DNA

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkr666

    DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.
    Figure Legend Snippet: DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.

    Techniques Used: Polyacrylamide Gel Electrophoresis, Marker

    25) Product Images from "Cooperative kinking at distant sites in mechanically stressed DNA"

    Article Title: Cooperative kinking at distant sites in mechanically stressed DNA

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkr666

    DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.
    Figure Legend Snippet: DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.

    Techniques Used: Polyacrylamide Gel Electrophoresis, Marker

    26) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    27) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    28) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    29) Product Images from "Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles"

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkp137

    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Figure Legend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Techniques Used: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).
    Figure Legend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Techniques Used: Agarose Gel Electrophoresis

    30) Product Images from "Cooperative kinking at distant sites in mechanically stressed DNA"

    Article Title: Cooperative kinking at distant sites in mechanically stressed DNA

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkr666

    DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.
    Figure Legend Snippet: DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.

    Techniques Used: Polyacrylamide Gel Electrophoresis, Marker

    31) Product Images from "Cooperative kinking at distant sites in mechanically stressed DNA"

    Article Title: Cooperative kinking at distant sites in mechanically stressed DNA

    Journal: Nucleic Acids Research

    doi: 10.1093/nar/gkr666

    DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.
    Figure Legend Snippet: DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.

    Techniques Used: Polyacrylamide Gel Electrophoresis, Marker

    32) Product Images from "Chromatin features of plant telomeric sequences at terminal vs. internal positions"

    Article Title: Chromatin features of plant telomeric sequences at terminal vs. internal positions

    Journal: Frontiers in Plant Science

    doi: 10.3389/fpls.2014.00593

    Internal localization of telomeric repeats in the B. antipoda genome. (A) High molecular weight DNA digested by Bal31 nuclease and a mix of frequently cutting restriction enzymes was analyzed by pulse field gel electrophoresis. Signals after hybridization with the radioactively labeled telomeric oligonucleotide showed resistance of telomeric sequences to Bal31 cleavage. The apparent decrease in signal intensity after 30 min of Bal31 digestion reflects variation in sample loading rather than a change due to the Bal31 treatment (compare to the signal after 45 min of Bal31). (B) DNA released into solution in the course of Bal31 digestions was purified and subjected to conventional agarose electrophoresis. The numbers above lines indicate the time of Bal31 digestion in minutes. M, DNA size markers.
    Figure Legend Snippet: Internal localization of telomeric repeats in the B. antipoda genome. (A) High molecular weight DNA digested by Bal31 nuclease and a mix of frequently cutting restriction enzymes was analyzed by pulse field gel electrophoresis. Signals after hybridization with the radioactively labeled telomeric oligonucleotide showed resistance of telomeric sequences to Bal31 cleavage. The apparent decrease in signal intensity after 30 min of Bal31 digestion reflects variation in sample loading rather than a change due to the Bal31 treatment (compare to the signal after 45 min of Bal31). (B) DNA released into solution in the course of Bal31 digestions was purified and subjected to conventional agarose electrophoresis. The numbers above lines indicate the time of Bal31 digestion in minutes. M, DNA size markers.

    Techniques Used: Molecular Weight, Nucleic Acid Electrophoresis, Hybridization, Labeling, Purification, Electrophoresis

    Relative cytosine methylation in telomeres of Nicotiana species. (A) After Bal31 treatment of N. tabacum high molecular weight DNA, TRF analysis was used to control the efficiency of digestion. A loss of the telomere-specific hybridization signal was observed in the course of Bal31 treatment. After 15 min of Bal31 digestion loss of the signal is evident but telomere erosion is not clear, whereas after 45- and 90-min treatments, telomeres were efficiently degraded. Time of Bal31 digestion is given above the lanes. M – DNA size marker. (B) Dot-blot analysis of Bal31-digested DNA from N. tabacum and N. tomentosiformis after treatment with sodium bisulfite. Samples were loaded onto a membrane and hybridized with radioactively labeled probes to detect the total signal of telomeres (loading probe pltel-C complementary to the telomeric G-strand) and the portion of methylated telomeres (DEGENER probe). Time of the Bal31 digestion in minutes is given above the membranes. +, positive hybridization control (tobacco DNA without the bisulfite treatment); −, negative control (DNA from the pUC19 plasmid). (C) Relative density of methylated cytosines along telomeres, calculated as the DEGENER/loading hybridization signals ratio. The ratio in Bal31 non-treated samples was arbitrarily taken as 1. Six independent experiments were performed.
    Figure Legend Snippet: Relative cytosine methylation in telomeres of Nicotiana species. (A) After Bal31 treatment of N. tabacum high molecular weight DNA, TRF analysis was used to control the efficiency of digestion. A loss of the telomere-specific hybridization signal was observed in the course of Bal31 treatment. After 15 min of Bal31 digestion loss of the signal is evident but telomere erosion is not clear, whereas after 45- and 90-min treatments, telomeres were efficiently degraded. Time of Bal31 digestion is given above the lanes. M – DNA size marker. (B) Dot-blot analysis of Bal31-digested DNA from N. tabacum and N. tomentosiformis after treatment with sodium bisulfite. Samples were loaded onto a membrane and hybridized with radioactively labeled probes to detect the total signal of telomeres (loading probe pltel-C complementary to the telomeric G-strand) and the portion of methylated telomeres (DEGENER probe). Time of the Bal31 digestion in minutes is given above the membranes. +, positive hybridization control (tobacco DNA without the bisulfite treatment); −, negative control (DNA from the pUC19 plasmid). (C) Relative density of methylated cytosines along telomeres, calculated as the DEGENER/loading hybridization signals ratio. The ratio in Bal31 non-treated samples was arbitrarily taken as 1. Six independent experiments were performed.

    Techniques Used: Methylation, Molecular Weight, Hybridization, Marker, Dot Blot, Labeling, Negative Control, Plasmid Preparation

    Methylation of cytosines of B. antipoda telomeric repeats. (A) Analysis of global methylation of cytosines in telomeric repeats of B. antipoda . High molecular weight DNA was treated with Bal31, converted with bisulfite and analyzed by Southern hybridization against loading and DEGENER probes. Signals with the DEGENER probe indicating methylated cytosines in telomeric repeats were obtained in all samples. The time of Bal31 digestion is given above the membranes. +, positive hybridization control (tobacco DNA without the bisulfite treatment); −, negative control (DNA from pUC19 plasmid). (B) An example of bisulfite sequencing data for Ba493 and Ba576 regions in adult leaves. Non-symmetrically located cytosines are depicted as green triangles; full triangle, methylated; empty triangle, non-methylated cytosine. Cytosines located in perfect telomeric repeats are underlined. The first line of the scheme where all cytosines in all sequence contexts are presented as full figures represents position of respective cytosine. (C) Graphical representation of telomeric cytosine methylation within the ITR-containing sequences Ba493 and Ba576. Three tissues were analyzed to reveal possible tissue-specific methylation pattern. “all,” all cytosines located in non-symmetrical sequence context; “telomeric,” cytosines located in perfect telomeric repeats. Data were processed by One-Way independent ANOVA test with standard weighted-means, * is used for P
    Figure Legend Snippet: Methylation of cytosines of B. antipoda telomeric repeats. (A) Analysis of global methylation of cytosines in telomeric repeats of B. antipoda . High molecular weight DNA was treated with Bal31, converted with bisulfite and analyzed by Southern hybridization against loading and DEGENER probes. Signals with the DEGENER probe indicating methylated cytosines in telomeric repeats were obtained in all samples. The time of Bal31 digestion is given above the membranes. +, positive hybridization control (tobacco DNA without the bisulfite treatment); −, negative control (DNA from pUC19 plasmid). (B) An example of bisulfite sequencing data for Ba493 and Ba576 regions in adult leaves. Non-symmetrically located cytosines are depicted as green triangles; full triangle, methylated; empty triangle, non-methylated cytosine. Cytosines located in perfect telomeric repeats are underlined. The first line of the scheme where all cytosines in all sequence contexts are presented as full figures represents position of respective cytosine. (C) Graphical representation of telomeric cytosine methylation within the ITR-containing sequences Ba493 and Ba576. Three tissues were analyzed to reveal possible tissue-specific methylation pattern. “all,” all cytosines located in non-symmetrical sequence context; “telomeric,” cytosines located in perfect telomeric repeats. Data were processed by One-Way independent ANOVA test with standard weighted-means, * is used for P

    Techniques Used: Methylation, Molecular Weight, Hybridization, Negative Control, Plasmid Preparation, Methylation Sequencing, Sequencing

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    Isolation:

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    Incubation:

    Article Title: The mitochondrial genome of the pathogenic yeast Candida subhashii: GC-rich linear DNA with a protein covalently attached to the 5? termini
    Article Snippet: The enzyme was inhibited by incubation in the presence of 5 mM EDTA (pH 7.5) at 70 °C for 10 min, and mtDNA was then purified using a NucleoSpin Extract II column (Macherey-Nagel). .. Approximately 1 μg mtDNA was treated with either exonuclease III (New England Biolabs) or BAL-31 nuclease (New England Biolabs) according to the manufacturer's instructions.

    Labeling:

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    Purification:

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    Electrophoresis:

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    Generated:

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    other:

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles
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    Activity Assay:

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    New England Biolabs bal31 nuclease
    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by <t>Bal31</t> (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.
    Bal31 Nuclease, supplied by New England Biolabs, used in various techniques. Bioz Stars score: 99/100, based on 3 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Journal: Nucleic Acids Research

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    doi: 10.1093/nar/gkp137

    Figure Lengend Snippet: The formation and purification of 94-bp-long covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that after the ligation reaction of minicircles with nicks, new species appear on the gel (compare lanes 3 with 2). Only these new species resist digestion by Bal31 (lane 4) indicating that they are covalently closed DNA molecules. The electrophoretic migration of these new species is as expected for monomeric, dimeric and trimeric rings that acquired writhe due to ethidium bromide intercalation to covalently closed DNA molecules.

    Article Snippet: However, the 94-bp-long minicircles with the sequence selected for their very efficient cyclization by C & W were not previously tested for their sensitivity to Bal31 nuclease.

    Techniques: Purification, Agarose Gel Electrophoresis, Ligation, Migration

    Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Journal: Nucleic Acids Research

    Article Title: Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

    doi: 10.1093/nar/gkp137

    Figure Lengend Snippet: Bal31 nuclease detects a destabilized duplex DNA structure in covalently closed supercoiled DNA molecules but does not reveal the presence of kinks in 94-bp covalently closed DNA minicircles. A 2.5% agarose gel run in the presence of ethidium bromide (0.5 µg/ml) reveals that while negatively supercoiled DNA (lane 6) and nonligated nicked rings are completely digested by Bal31 nuclease (see lanes 2–4), the covalently closed monomeric, dimerc, trimeric and tetrameric circles (indicated with arrows) remain resistant to action of Bal31 nuclease (compare lanes 4 and 3).

    Article Snippet: However, the 94-bp-long minicircles with the sequence selected for their very efficient cyclization by C & W were not previously tested for their sensitivity to Bal31 nuclease.

    Techniques: Agarose Gel Electrophoresis

    DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.

    Journal: Nucleic Acids Research

    Article Title: Cooperative kinking at distant sites in mechanically stressed DNA

    doi: 10.1093/nar/gkr666

    Figure Lengend Snippet: DNA minicircles with 100, 106 and 108 bp, their purity and their susceptibility to Bal31 digestion. In a 10% denaturing PAGE gel (7 M urea), the denatured linear DNA fragments used as a marker, migrate much quicker than circular, covalently closed DNA minicircles in which the two strands cannot separate in space. Notice the presence of only one topoisomer in each category of minicircles and the sensitivity of minicircles with 100 bp to Bal31 nuclease.

    Article Snippet: This result indicates that the negative torsional stress sustained within MC100, previously shown to result in sensitivity to Bal31 nuclease, also leads to the creation of easily bendable sites that permit the molecules to minimize their bending energy by adopting elongated, elliptical shapes.

    Techniques: Polyacrylamide Gel Electrophoresis, Marker

    CNDCA-based production of supercoiled minicircle. Image of stained native polyacrylamide gel showing 95 bp minicircle topoisomers of decreased linking number (ΔLk values of −1 and −2) (lanes 4, 6) as indicated on the right and obtained by religation of the nicked minicircle in the presence of EtBr. The slowest migrating band corresponds to the relaxed minicircle that migrates expectedly at the same rate as the nicked minicircle (lanes 1 and 2). Digestion of minicircle samples by the nuclease Bal31 is indicated on the right. The position of the molecular mass markers in bp is indicated on the left.

    Journal: Nucleic Acids Research

    Article Title: Production of DNA minicircles less than 250 base pairs through a novel concentrated DNA circularization assay enabling minicircle design with NF-κB inhibition activity

    doi: 10.1093/nar/gkw1034

    Figure Lengend Snippet: CNDCA-based production of supercoiled minicircle. Image of stained native polyacrylamide gel showing 95 bp minicircle topoisomers of decreased linking number (ΔLk values of −1 and −2) (lanes 4, 6) as indicated on the right and obtained by religation of the nicked minicircle in the presence of EtBr. The slowest migrating band corresponds to the relaxed minicircle that migrates expectedly at the same rate as the nicked minicircle (lanes 1 and 2). Digestion of minicircle samples by the nuclease Bal31 is indicated on the right. The position of the molecular mass markers in bp is indicated on the left.

    Article Snippet: We next used Bal31 nuclease to detect the presence of DNA distortions within our constrained minicircles.

    Techniques: Staining