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GenScript corporation human ape1 complementary dna (cdna)

Orphan base preference in plant and bacterial AP endonucleases. ( A ) Opposite base preference in a single sequence context. <t>APE1</t> (0.02 nM), ARP (40 nM), ExoIII (0.06 nM) or EndoIV (0.3 nM) were incubated with <t>DNA</t> substrates (20 nM) containing a native AP site opposite G (orange), A (green), T (yellow) or C (blue) in the sequence context 5′-A X G-3′ ( X = AP site). ( B ) Opposite base preference in different sequence contexts. DNA substrates (20 nM) containing a native AP site opposite G (orange) or C (blue) in four different sequence contexts were incubated with APE1 (0.01 nM), ARP (40 nM), ExoIII (0.06 nM) or EndoIV (0.9 nM). The reaction products were stabilized with NaBH 4 , separated by denaturing PAGE and detected by fluorescence scanning for quantification. Data are the mean and standard error from two independent experiments. Asterisks indicate significant differences in a two-tailed Student’s t -test (* P < 0.05; ** P < 0.01; *** P < 0.001).

Human Ape1 Complementary Dna (Cdna), supplied by GenScript corporation, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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1) Product Images from "Divergent evolution of opposite base specificity and single-stranded DNA activity in animal and plant AP endonucleases"

Article Title: Divergent evolution of opposite base specificity and single-stranded DNA activity in animal and plant AP endonucleases

Journal: Nucleic Acids Research

doi: 10.1093/nar/gkae1297

Orphan base preference in plant and bacterial AP endonucleases. ( A ) Opposite base preference in a single sequence context. APE1 (0.02 nM), ARP (40 nM), ExoIII (0.06 nM) or EndoIV (0.3 nM) were incubated with DNA substrates (20 nM) containing a native AP site opposite G (orange), A (green), T (yellow) or C (blue) in the sequence context 5′-A X G-3′ ( X = AP site). ( B ) Opposite base preference in different sequence contexts. DNA substrates (20 nM) containing a native AP site opposite G (orange) or C (blue) in four different sequence contexts were incubated with APE1 (0.01 nM), ARP (40 nM), ExoIII (0.06 nM) or EndoIV (0.9 nM). The reaction products were stabilized with NaBH 4 , separated by denaturing PAGE and detected by fluorescence scanning for quantification. Data are the mean and standard error from two independent experiments. Asterisks indicate significant differences in a two-tailed Student’s t -test (* P < 0.05; ** P < 0.01; *** P < 0.001).

Figure Legend Snippet: Orphan base preference in plant and bacterial AP endonucleases. ( A ) Opposite base preference in a single sequence context. APE1 (0.02 nM), ARP (40 nM), ExoIII (0.06 nM) or EndoIV (0.3 nM) were incubated with DNA substrates (20 nM) containing a native AP site opposite G (orange), A (green), T (yellow) or C (blue) in the sequence context 5′-A X G-3′ ( X = AP site). ( B ) Opposite base preference in different sequence contexts. DNA substrates (20 nM) containing a native AP site opposite G (orange) or C (blue) in four different sequence contexts were incubated with APE1 (0.01 nM), ARP (40 nM), ExoIII (0.06 nM) or EndoIV (0.9 nM). The reaction products were stabilized with NaBH 4 , separated by denaturing PAGE and detected by fluorescence scanning for quantification. Data are the mean and standard error from two independent experiments. Asterisks indicate significant differences in a two-tailed Student’s t -test (* P < 0.05; ** P < 0.01; *** P < 0.001).

Techniques Used: Sequencing, Incubation, Fluorescence, Two Tailed Test

Divergent conservation of two DNA intercalating residues in APE1 orthologs. ( A ) Domain organization in human APE1, Arabidopsis ARP and E. coli ExoIII. ( B ) Structural superimposition of the double DNA insertion loops of APE1–DNA complex (PDB code: 5DFF) and ARP–DNA complex (PDB code: 8KA3). ( C ) Multiple sequence alignment of 25 representative APE1 orthologs showing the positions of the two DNA intercalating residues. ( D ) Amino acid frequencies in the two DNA insertion loops in APE1 orthologs from 2386 bacteria, 436 archaea, 242 fungi, 182 plants and 462 metazoans displayed as sequence logos generated by WebLogo 3.

Figure Legend Snippet: Divergent conservation of two DNA intercalating residues in APE1 orthologs. ( A ) Domain organization in human APE1, Arabidopsis ARP and E. coli ExoIII. ( B ) Structural superimposition of the double DNA insertion loops of APE1–DNA complex (PDB code: 5DFF) and ARP–DNA complex (PDB code: 8KA3). ( C ) Multiple sequence alignment of 25 representative APE1 orthologs showing the positions of the two DNA intercalating residues. ( D ) Amino acid frequencies in the two DNA insertion loops in APE1 orthologs from 2386 bacteria, 436 archaea, 242 fungi, 182 plants and 462 metazoans displayed as sequence logos generated by WebLogo 3.

Techniques Used: Sequencing, Bacteria, Generated

The opposite base preferences of APE1 and ARP are switched by exchanging the identity of the residue invading the minor groove. Different mutant versions of APE1 (0.2 nM) or ARP (40 nM) were incubated with DNA substrates (20 nM) containing a synthetic AP site (THF) opposite G (orange), A (green), T (yellow) or C (blue) in the sequence context 5′-A X G-3′ ( X = AP site). The reaction products were separated by denaturing PAGE, and detected by fluorescence scanning for quantification. Data are the mean and standard error from two independent experiments.

Figure Legend Snippet: The opposite base preferences of APE1 and ARP are switched by exchanging the identity of the residue invading the minor groove. Different mutant versions of APE1 (0.2 nM) or ARP (40 nM) were incubated with DNA substrates (20 nM) containing a synthetic AP site (THF) opposite G (orange), A (green), T (yellow) or C (blue) in the sequence context 5′-A X G-3′ ( X = AP site). The reaction products were separated by denaturing PAGE, and detected by fluorescence scanning for quantification. Data are the mean and standard error from two independent experiments.

Techniques Used: Residue, Mutagenesis, Incubation, Sequencing, Fluorescence

$Orphan base-dependent dissociation of ARP from its reaction product. ( A ) Schematic diagram of labelled DNA duplexes used as probes in the electrophoretic mobility shift assay (EMSA). The orphan base is indicated as S (= G or C). ( B ) EMSA. Increasing concentrations of APE1 or ARPΔ139 were incubated at 25°C for 25 min with Fl-labelled probes (10 nM) containing G or C as orphan base. After nondenaturing electrophoresis, free DNA (F) and protein–DNA complexes (bound DNA; B) were detected by fluorescence scanning. ( C ) Quantification of the fraction of bound DNA. The fraction of bound DNA with G (orange) or C (blue) as orphan base is plotted against protein concentration. Data are the mean and standard error from two independent experiments.$
Figure Legend Snippet: Orphan base-dependent dissociation of ARP from its reaction product. ( A ) Schematic diagram of labelled DNA duplexes used as probes in the electrophoretic mobility shift assay (EMSA). The orphan base is indicated as S (= G or C). ( B ) EMSA. Increasing concentrations of APE1 or ARPΔ139 were incubated at 25°C for 25 min with Fl-labelled probes (10 nM) containing G or C as orphan base. After nondenaturing electrophoresis, free DNA (F) and protein–DNA complexes (bound DNA; B) were detected by fluorescence scanning. ( C ) Quantification of the fraction of bound DNA. The fraction of bound DNA with G (orange) or C (blue) as orphan base is plotted against protein concentration. Data are the mean and standard error from two independent experiments.

Techniques Used: Electrophoretic Mobility Shift Assay, Incubation, Electrophoresis, Fluorescence, Protein Concentration

Binding affinity of WT and mutant versions of APE1 and ARPΔ139 for dsDNA substrates and products with different orphan bases

Figure Legend Snippet: Binding affinity of WT and mutant versions of APE1 and ARPΔ139 for dsDNA substrates and products with different orphan bases

Techniques Used: Binding Assay, Mutagenesis

Exchanging the identity of the residue invading the major groove is sufficient to interconvert the activities of APE1 and ARP in ssDNA. ( A ) Schematic diagram of labelled DNA molecules used as dsDNA and ssDNA substrates. The AP site (THF) is indicated in red. ( B ) Different mutant versions of APE1 (0.2 nM) or ARP (40 nM) were incubated with dsDNA (pink) or ssDNA (purple) substrates (20 nM). The reaction products were separated by denaturing PAGE, detected by fluorescence scanning and quantified. Data are the mean and standard error from two independent experiments.

Figure Legend Snippet: Exchanging the identity of the residue invading the major groove is sufficient to interconvert the activities of APE1 and ARP in ssDNA. ( A ) Schematic diagram of labelled DNA molecules used as dsDNA and ssDNA substrates. The AP site (THF) is indicated in red. ( B ) Different mutant versions of APE1 (0.2 nM) or ARP (40 nM) were incubated with dsDNA (pink) or ssDNA (purple) substrates (20 nM). The reaction products were separated by denaturing PAGE, detected by fluorescence scanning and quantified. Data are the mean and standard error from two independent experiments.

Techniques Used: Residue, Mutagenesis, Incubation, Fluorescence

$Affinity for ssDNA is largely determined by the residue that intercalates into the major groove. ( A ) EMSA. Increasing concentrations of WT APE1 or ARPΔ139 were incubated at 25°C for 25 min with a Fl-labelled ssDNA probe (10 nM). After nondenaturing electrophoresis, free DNA (F) and protein–DNA complexes (bound DNA; B) were detected by fluorescence scanning. ( B ) The fraction of DNA bound to WT and mutant versions of APE1 or ARPΔ139 is plotted against protein concentration. Data are the mean and standard error from two independent experiments.$
Figure Legend Snippet: Affinity for ssDNA is largely determined by the residue that intercalates into the major groove. ( A ) EMSA. Increasing concentrations of WT APE1 or ARPΔ139 were incubated at 25°C for 25 min with a Fl-labelled ssDNA probe (10 nM). After nondenaturing electrophoresis, free DNA (F) and protein–DNA complexes (bound DNA; B) were detected by fluorescence scanning. ( B ) The fraction of DNA bound to WT and mutant versions of APE1 or ARPΔ139 is plotted against protein concentration. Data are the mean and standard error from two independent experiments.

Techniques Used: Residue, Incubation, Electrophoresis, Fluorescence, Mutagenesis, Protein Concentration

Figure Legend Snippet: Binding affinity of WT and mutant versions of APE1 and ARPΔ139 for ssDNA

Techniques Used: Binding Assay, Mutagenesis

Figure Legend Snippet: The residue that invades the major groove is critical for mammalian APE1 function in antibody CSR. The relative percentage of IgA on the surface of CH12F3_APE1 Δ/Δ/Δ ( A ), or CH12F3_APE1 Δ/Δ/Δ APE2 Y/Δ ( B ) cells was measured after transient transfection with different mAPE1 constructs and CIT stimulation during 72 h. Data are the mean and standard error from five (panel A) or three (panel B) independent experiments. Asterisks indicate significant differences in a two-tailed Student’s t -test (* P < 0.05; ** P < 0.01; *** P < 0.001). Protein expression of the different mAPE1 variants was determined by western blot (upper panels). ( C ) Representative flow cytometry profile of the IgA switching population of CH12F3_ APE1 Δ/Δ/Δ cells after 72 h of cell growth under CIT− or CIT+ conditions.

Techniques Used: Residue, Transfection, Construct, Two Tailed Test, Expressing, Western Blot, Flow Cytometry

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Journal: Nucleic Acids Research

Article Title: Divergent evolution of opposite base specificity and single-stranded DNA activity in animal and plant AP endonucleases

doi: 10.1093/nar/gkae1297

Figure Lengend Snippet: Orphan base preference in plant and bacterial AP endonucleases. ( A ) Opposite base preference in a single sequence context. APE1 (0.02 nM), ARP (40 nM), ExoIII (0.06 nM) or EndoIV (0.3 nM) were incubated with DNA substrates (20 nM) containing a native AP site opposite G (orange), A (green), T (yellow) or C (blue) in the sequence context 5′-A X G-3′ ( X = AP site). ( B ) Opposite base preference in different sequence contexts. DNA substrates (20 nM) containing a native AP site opposite G (orange) or C (blue) in four different sequence contexts were incubated with APE1 (0.01 nM), ARP (40 nM), ExoIII (0.06 nM) or EndoIV (0.9 nM). The reaction products were stabilized with NaBH 4 , separated by denaturing PAGE and detected by fluorescence scanning for quantification. Data are the mean and standard error from two independent experiments. Asterisks indicate significant differences in a two-tailed Student’s t -test (* P < 0.05; ** P < 0.01; *** P < 0.001).

Article Snippet: Human APE1 complementary DNA (cDNA) was synthetized by codon optimization for expression in bacteria (GenScript).

Techniques: Sequencing, Incubation, Fluorescence, Two Tailed Test

Journal: Nucleic Acids Research

Article Title: Divergent evolution of opposite base specificity and single-stranded DNA activity in animal and plant AP endonucleases

doi: 10.1093/nar/gkae1297

Figure Lengend Snippet: Divergent conservation of two DNA intercalating residues in APE1 orthologs. ( A ) Domain organization in human APE1, Arabidopsis ARP and E. coli ExoIII. ( B ) Structural superimposition of the double DNA insertion loops of APE1–DNA complex (PDB code: 5DFF) and ARP–DNA complex (PDB code: 8KA3). ( C ) Multiple sequence alignment of 25 representative APE1 orthologs showing the positions of the two DNA intercalating residues. ( D ) Amino acid frequencies in the two DNA insertion loops in APE1 orthologs from 2386 bacteria, 436 archaea, 242 fungi, 182 plants and 462 metazoans displayed as sequence logos generated by WebLogo 3.

Article Snippet: Human APE1 complementary DNA (cDNA) was synthetized by codon optimization for expression in bacteria (GenScript).

Techniques: Sequencing, Bacteria, Generated

Journal: Nucleic Acids Research

Article Title: Divergent evolution of opposite base specificity and single-stranded DNA activity in animal and plant AP endonucleases

doi: 10.1093/nar/gkae1297

Figure Lengend Snippet: The opposite base preferences of APE1 and ARP are switched by exchanging the identity of the residue invading the minor groove. Different mutant versions of APE1 (0.2 nM) or ARP (40 nM) were incubated with DNA substrates (20 nM) containing a synthetic AP site (THF) opposite G (orange), A (green), T (yellow) or C (blue) in the sequence context 5′-A X G-3′ ( X = AP site). The reaction products were separated by denaturing PAGE, and detected by fluorescence scanning for quantification. Data are the mean and standard error from two independent experiments.

Article Snippet: Human APE1 complementary DNA (cDNA) was synthetized by codon optimization for expression in bacteria (GenScript).

Techniques: Residue, Mutagenesis, Incubation, Sequencing, Fluorescence

Journal: Nucleic Acids Research

Article Title: Divergent evolution of opposite base specificity and single-stranded DNA activity in animal and plant AP endonucleases

doi: 10.1093/nar/gkae1297

Figure Lengend Snippet: Orphan base-dependent dissociation of ARP from its reaction product. ( A ) Schematic diagram of labelled DNA duplexes used as probes in the electrophoretic mobility shift assay (EMSA). The orphan base is indicated as S (= G or C). ( B ) EMSA. Increasing concentrations of APE1 or ARPΔ139 were incubated at 25°C for 25 min with Fl-labelled probes (10 nM) containing G or C as orphan base. After nondenaturing electrophoresis, free DNA (F) and protein–DNA complexes (bound DNA; B) were detected by fluorescence scanning. ( C ) Quantification of the fraction of bound DNA. The fraction of bound DNA with G (orange) or C (blue) as orphan base is plotted against protein concentration. Data are the mean and standard error from two independent experiments.

Article Snippet: Human APE1 complementary DNA (cDNA) was synthetized by codon optimization for expression in bacteria (GenScript).

Techniques: Electrophoretic Mobility Shift Assay, Incubation, Electrophoresis, Fluorescence, Protein Concentration

Journal: Nucleic Acids Research

Article Title: Divergent evolution of opposite base specificity and single-stranded DNA activity in animal and plant AP endonucleases

doi: 10.1093/nar/gkae1297

Figure Lengend Snippet: Binding affinity of WT and mutant versions of APE1 and ARPΔ139 for dsDNA substrates and products with different orphan bases

Article Snippet: Human APE1 complementary DNA (cDNA) was synthetized by codon optimization for expression in bacteria (GenScript).

Techniques: Binding Assay, Mutagenesis

Journal: Nucleic Acids Research

Article Title: Divergent evolution of opposite base specificity and single-stranded DNA activity in animal and plant AP endonucleases

doi: 10.1093/nar/gkae1297

Figure Lengend Snippet: Exchanging the identity of the residue invading the major groove is sufficient to interconvert the activities of APE1 and ARP in ssDNA. ( A ) Schematic diagram of labelled DNA molecules used as dsDNA and ssDNA substrates. The AP site (THF) is indicated in red. ( B ) Different mutant versions of APE1 (0.2 nM) or ARP (40 nM) were incubated with dsDNA (pink) or ssDNA (purple) substrates (20 nM). The reaction products were separated by denaturing PAGE, detected by fluorescence scanning and quantified. Data are the mean and standard error from two independent experiments.

Article Snippet: Human APE1 complementary DNA (cDNA) was synthetized by codon optimization for expression in bacteria (GenScript).

Techniques: Residue, Mutagenesis, Incubation, Fluorescence

Journal: Nucleic Acids Research

Article Title: Divergent evolution of opposite base specificity and single-stranded DNA activity in animal and plant AP endonucleases

doi: 10.1093/nar/gkae1297

Figure Lengend Snippet: Affinity for ssDNA is largely determined by the residue that intercalates into the major groove. ( A ) EMSA. Increasing concentrations of WT APE1 or ARPΔ139 were incubated at 25°C for 25 min with a Fl-labelled ssDNA probe (10 nM). After nondenaturing electrophoresis, free DNA (F) and protein–DNA complexes (bound DNA; B) were detected by fluorescence scanning. ( B ) The fraction of DNA bound to WT and mutant versions of APE1 or ARPΔ139 is plotted against protein concentration. Data are the mean and standard error from two independent experiments.

Article Snippet: Human APE1 complementary DNA (cDNA) was synthetized by codon optimization for expression in bacteria (GenScript).

Techniques: Residue, Incubation, Electrophoresis, Fluorescence, Mutagenesis, Protein Concentration

Journal: Nucleic Acids Research

Article Title: Divergent evolution of opposite base specificity and single-stranded DNA activity in animal and plant AP endonucleases

doi: 10.1093/nar/gkae1297

Figure Lengend Snippet: Binding affinity of WT and mutant versions of APE1 and ARPΔ139 for ssDNA

Article Snippet: Human APE1 complementary DNA (cDNA) was synthetized by codon optimization for expression in bacteria (GenScript).

Techniques: Binding Assay, Mutagenesis

Journal: Nucleic Acids Research

Article Title: Divergent evolution of opposite base specificity and single-stranded DNA activity in animal and plant AP endonucleases

doi: 10.1093/nar/gkae1297

Figure Lengend Snippet: The residue that invades the major groove is critical for mammalian APE1 function in antibody CSR. The relative percentage of IgA on the surface of CH12F3_APE1 Δ/Δ/Δ ( A ), or CH12F3_APE1 Δ/Δ/Δ APE2 Y/Δ ( B ) cells was measured after transient transfection with different mAPE1 constructs and CIT stimulation during 72 h. Data are the mean and standard error from five (panel A) or three (panel B) independent experiments. Asterisks indicate significant differences in a two-tailed Student’s t -test (* P < 0.05; ** P < 0.01; *** P < 0.001). Protein expression of the different mAPE1 variants was determined by western blot (upper panels). ( C ) Representative flow cytometry profile of the IgA switching population of CH12F3_ APE1 Δ/Δ/Δ cells after 72 h of cell growth under CIT− or CIT+ conditions.

Article Snippet: Human APE1 complementary DNA (cDNA) was synthetized by codon optimization for expression in bacteria (GenScript).

Techniques: Residue, Transfection, Construct, Two Tailed Test, Expressing, Western Blot, Flow Cytometry

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