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biomers.net primer sequences
Primer Sequences, supplied by biomers.net, used in various techniques. Bioz Stars score: 92/100, based on 7 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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primer sequences - by Bioz Stars, 2020-07
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Real-time Polymerase Chain Reaction:

Article Title: PD-L1 Expression on Retrovirus-Infected Cells Mediates Immune Escape from CD8+ T Cell Killing
Article Snippet: .. Real time-PCR analysis for the quantification of IFN-α mRNA was performed using Power SYBR Green RT-PCR kit (Life Technologies) Primer sequences (Biomers) were as follows: 5’-atggctaggctctgtgctttcct-3’, 5’-agggctctccagacttctgctctg-3’. .. The absolute mRNA copy numbers were determined by using StepOne Software v2.3 (Life Technologies).

Article Title: Platelet lysate outperforms FCS and human serum for co-culture of primary human macrophages and hMSCs
Article Snippet: .. For the amplification of the mRNA, each 10 µl qPCR reaction comprised 5 ng of cDNA and 200 nM primer sequences (Biomers, Ulm (D)) (Table ). .. For each cDNA sample, the threshold cycle (Ct) value of each target sequence was subtracted from the Ct value of the house keeping mRNA RPS27a, to derive ΔCt.

SYBR Green Assay:

Article Title: PD-L1 Expression on Retrovirus-Infected Cells Mediates Immune Escape from CD8+ T Cell Killing
Article Snippet: .. Real time-PCR analysis for the quantification of IFN-α mRNA was performed using Power SYBR Green RT-PCR kit (Life Technologies) Primer sequences (Biomers) were as follows: 5’-atggctaggctctgtgctttcct-3’, 5’-agggctctccagacttctgctctg-3’. .. The absolute mRNA copy numbers were determined by using StepOne Software v2.3 (Life Technologies).

Amplification:

Article Title: Platelet lysate outperforms FCS and human serum for co-culture of primary human macrophages and hMSCs
Article Snippet: .. For the amplification of the mRNA, each 10 µl qPCR reaction comprised 5 ng of cDNA and 200 nM primer sequences (Biomers, Ulm (D)) (Table ). .. For each cDNA sample, the threshold cycle (Ct) value of each target sequence was subtracted from the Ct value of the house keeping mRNA RPS27a, to derive ΔCt.

Reverse Transcription Polymerase Chain Reaction:

Article Title: PD-L1 Expression on Retrovirus-Infected Cells Mediates Immune Escape from CD8+ T Cell Killing
Article Snippet: .. Real time-PCR analysis for the quantification of IFN-α mRNA was performed using Power SYBR Green RT-PCR kit (Life Technologies) Primer sequences (Biomers) were as follows: 5’-atggctaggctctgtgctttcct-3’, 5’-agggctctccagacttctgctctg-3’. .. The absolute mRNA copy numbers were determined by using StepOne Software v2.3 (Life Technologies).

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  • 92
    biomers.net fluc
    Knockdown efficiencies of different miRNA designs. ( A ) Sequences and secondary structures of different miRNA designs. Boxed sequences are the double-stranded RNA sequences matching the target site within the firefly luciferase <t>(fluc)</t> mRNA. Added or modified sequence elements from miRNA1 to miRNA3 are explicitly labelled. Dicer: Dicer cleavage sequences ( 30 ). Drosha/Exportin 5: Sequences for cleavage by Drosha and nuclear export signal by Exportin 5 ( 15 ). Dicer 2: Dicer cleavage loop as used in miB-tat in Boden et al . ( 31 ). ( B–G ) Quantification of knockdown efficiencies of differently designed miRNAs, expressed from either the pol III promoter P H1 (B–D) or the pol II promoter P CMV (E–G). Relative fluc activities (B and E), relative fluc mRNA concentrations (C and F) and the concentrations of mature miRNA (D and G) were determined in cell extracts from individual transient expression experiments. The results in B and E were normalized to activity and in C and F to mRNA concentration of <t>rluc,</t> produced from the SV40 promoter within the co-transfected expression vector. Figures B–G show the means and SEM from multiple samples of at least two independent transfection experiments. (A) n 1: SV40 polyadenylation signal. TTTTT: pol III termination signal.
    Fluc, supplied by biomers.net, used in various techniques. Bioz Stars score: 92/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    91
    biomers.net abl1 copy number assessment
    Outcome of patients according to pre-HSCT BAALC / <t>ABL1</t> copy numbers, high vs low, 0. 14 cut, (A) Cumulative Incidence of Relapse and (B) Overall Survival for the entire set (n=82) and (C) Cumulative Incidence of relapse and (D) Overall Survival in patients with a normal karyotype (n=38).
    Abl1 Copy Number Assessment, supplied by biomers.net, used in various techniques. Bioz Stars score: 91/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/abl1 copy number assessment/product/biomers.net
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    85
    biomers.net aptamer selection process
    SPR interaction analyses applying the aptamers PA#2/8 and PA#2/8[S1-58] as analyte. Biacore X100 / sensor chip CAP / ligand: biotinylated native Protein A with immobilization level of ~600 RU / analyte: 5’-fluorescein-labeled <t>aptamer</t> PA#2/8 (A) or truncated variant PA#2/8[S1-58] (C) with different concentrations (250–8000 nM, 2000 nM in triplicate). Double-referenced sensorgrams are shown (blank reference surface without Protein A, buffer injection). Black lines represent the fit to 1:1 binding model. The corresponding plots (B, D) of steady-state binding from the end of the association phases against analyte concentration are used to calculate the steady-state affinity.
    Aptamer Selection Process, supplied by biomers.net, used in various techniques. Bioz Stars score: 85/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Knockdown efficiencies of different miRNA designs. ( A ) Sequences and secondary structures of different miRNA designs. Boxed sequences are the double-stranded RNA sequences matching the target site within the firefly luciferase (fluc) mRNA. Added or modified sequence elements from miRNA1 to miRNA3 are explicitly labelled. Dicer: Dicer cleavage sequences ( 30 ). Drosha/Exportin 5: Sequences for cleavage by Drosha and nuclear export signal by Exportin 5 ( 15 ). Dicer 2: Dicer cleavage loop as used in miB-tat in Boden et al . ( 31 ). ( B–G ) Quantification of knockdown efficiencies of differently designed miRNAs, expressed from either the pol III promoter P H1 (B–D) or the pol II promoter P CMV (E–G). Relative fluc activities (B and E), relative fluc mRNA concentrations (C and F) and the concentrations of mature miRNA (D and G) were determined in cell extracts from individual transient expression experiments. The results in B and E were normalized to activity and in C and F to mRNA concentration of rluc, produced from the SV40 promoter within the co-transfected expression vector. Figures B–G show the means and SEM from multiple samples of at least two independent transfection experiments. (A) n 1: SV40 polyadenylation signal. TTTTT: pol III termination signal.

    Journal: Nucleic Acids Research

    Article Title: Quantitative analysis of conditional gene inactivation using rationally designed, tetracycline-controlled miRNAs

    doi: 10.1093/nar/gkq616

    Figure Lengend Snippet: Knockdown efficiencies of different miRNA designs. ( A ) Sequences and secondary structures of different miRNA designs. Boxed sequences are the double-stranded RNA sequences matching the target site within the firefly luciferase (fluc) mRNA. Added or modified sequence elements from miRNA1 to miRNA3 are explicitly labelled. Dicer: Dicer cleavage sequences ( 30 ). Drosha/Exportin 5: Sequences for cleavage by Drosha and nuclear export signal by Exportin 5 ( 15 ). Dicer 2: Dicer cleavage loop as used in miB-tat in Boden et al . ( 31 ). ( B–G ) Quantification of knockdown efficiencies of differently designed miRNAs, expressed from either the pol III promoter P H1 (B–D) or the pol II promoter P CMV (E–G). Relative fluc activities (B and E), relative fluc mRNA concentrations (C and F) and the concentrations of mature miRNA (D and G) were determined in cell extracts from individual transient expression experiments. The results in B and E were normalized to activity and in C and F to mRNA concentration of rluc, produced from the SV40 promoter within the co-transfected expression vector. Figures B–G show the means and SEM from multiple samples of at least two independent transfection experiments. (A) n 1: SV40 polyadenylation signal. TTTTT: pol III termination signal.

    Article Snippet: For simultaneous detection of fluc and rluc mRNA, the following primers and probes were used: fluc forward primer 5′-TGTGGACGAAGTACCGAAAGGT-3′; fluc reverse primer 5′-CTTCTTGGCCTTTATGAGGATCTC-3′; fluc probe 5′-FAM-CCGGAAAACTC-GACGCAAGAAAAATCAG-TAMRA-3′; rluc forward primer 5′-AAAGGTGAAGTTCGT-CGTCCA-3′; rluc reverse primer 5′-CAACGTCAGGTTTACCACCTTTT-3′; rluc probe 5′-HEX-CATTATCATGGCCTCGTGAAATCCCGT-TAMRA-3′ (FAM: 6-carboxy-fluoresceine; HEX: hexachloro-fluoresceine; TAMRA: 6-carboxy-tetramethyl-rhodamine; biomers.net).

    Techniques: Luciferase, Modification, Sequencing, Expressing, Activity Assay, Concentration Assay, Produced, Transfection, Plasmid Preparation

    Activation kinetic of tet-regulated miRNA3-mediated gene knockdown in Tet-Off cell line HtTA 16-1. Tet-regulated expression of miRNA3(FL-B) and rluc was started in cell line HtTA16-1 (utilizing the Tet Off system) by removal of dox from the culture medium. Activation of tet-regulated transcription of miRNA3(FL-B) and miRNA-mediated knockdown of fluc was monitored over a period of 130 h by quantifying rluc ( A ) and fluc ( D ) activity, relative rluc ( B ) and fluc ( E ) mRNA concentration and the concentration of mature miRNA ( C ) in the samples of HtTA 16-1 cells collected at the indicated time points. Both luciferase activities were normalized to total protein concentration, mRNA and miRNA concentrations to the concentration of β-actin mRNA. Figures show means with SEM of multiple samples from two independent experiments.

    Journal: Nucleic Acids Research

    Article Title: Quantitative analysis of conditional gene inactivation using rationally designed, tetracycline-controlled miRNAs

    doi: 10.1093/nar/gkq616

    Figure Lengend Snippet: Activation kinetic of tet-regulated miRNA3-mediated gene knockdown in Tet-Off cell line HtTA 16-1. Tet-regulated expression of miRNA3(FL-B) and rluc was started in cell line HtTA16-1 (utilizing the Tet Off system) by removal of dox from the culture medium. Activation of tet-regulated transcription of miRNA3(FL-B) and miRNA-mediated knockdown of fluc was monitored over a period of 130 h by quantifying rluc ( A ) and fluc ( D ) activity, relative rluc ( B ) and fluc ( E ) mRNA concentration and the concentration of mature miRNA ( C ) in the samples of HtTA 16-1 cells collected at the indicated time points. Both luciferase activities were normalized to total protein concentration, mRNA and miRNA concentrations to the concentration of β-actin mRNA. Figures show means with SEM of multiple samples from two independent experiments.

    Article Snippet: For simultaneous detection of fluc and rluc mRNA, the following primers and probes were used: fluc forward primer 5′-TGTGGACGAAGTACCGAAAGGT-3′; fluc reverse primer 5′-CTTCTTGGCCTTTATGAGGATCTC-3′; fluc probe 5′-FAM-CCGGAAAACTC-GACGCAAGAAAAATCAG-TAMRA-3′; rluc forward primer 5′-AAAGGTGAAGTTCGT-CGTCCA-3′; rluc reverse primer 5′-CAACGTCAGGTTTACCACCTTTT-3′; rluc probe 5′-HEX-CATTATCATGGCCTCGTGAAATCCCGT-TAMRA-3′ (FAM: 6-carboxy-fluoresceine; HEX: hexachloro-fluoresceine; TAMRA: 6-carboxy-tetramethyl-rhodamine; biomers.net).

    Techniques: Activation Assay, Expressing, Activity Assay, Concentration Assay, Luciferase, Protein Concentration

    Simultaneous gene inactivation of multiple genes by tandem-arrayed miRNAs. ( A ) Schematic representation of sequences present in expression vectors with tandem-arrayed miRNAs. P tet–1 , tet-regulatable promoter; (A) n 1, SV40 polyadenylation signal. Brackets show the size of the non-coding linker sequence separating the individual miRNAs of the type miRNA3. ( B ) Firefly (fluc) and renilla (rluc) luciferase activities were quantified in a co-transfection experiment, in which the constitutive production of firefly and renilla luciferase from respective expression vectors was inhibited by the indicated expression vector bearing a tet-regulated miRNA3 cassette. Measured luciferase activities were normalized to the present fluorescence intensity of eGFP, which was expressed under control of P CMV from an additional co-transfected expression plasmid. Structure of tandem expression vectors is described in (A) FL-B: expression vector with miRNA3(FL-B) under control of P tet–1 . RL-A, expression vector with miRNA3(RL-A) under control of P tet–1 ; FL-B + RL-A, co-transfection of two expression vectors containing either miRNA3(FL-B) or miRNA3(RL-A) under control of P tet–1 . ( C ) Rluc activities were determined in a co-transfection experiment, in which the constitutive production of renilla luciferase was inhibited by the indicated vectors and normalized to fluc activity. RL-A, RL-B, RL-C: expression vectors with a single miRNA3 targeting rluc at a particular sequence (A or B or C) under control of P tet–1 . Tandem bicistronic constructs follow the nomenclature as described in (A). RL-A+ RL-C: co-transfection of two expression vectors containing either a single miRNA3(RL-A) or a single miRNA3(RL-C) under the control of P tet–1 . Figures B and C show means and SEM from multiple samples taken from at least two independent transfection experiments.

    Journal: Nucleic Acids Research

    Article Title: Quantitative analysis of conditional gene inactivation using rationally designed, tetracycline-controlled miRNAs

    doi: 10.1093/nar/gkq616

    Figure Lengend Snippet: Simultaneous gene inactivation of multiple genes by tandem-arrayed miRNAs. ( A ) Schematic representation of sequences present in expression vectors with tandem-arrayed miRNAs. P tet–1 , tet-regulatable promoter; (A) n 1, SV40 polyadenylation signal. Brackets show the size of the non-coding linker sequence separating the individual miRNAs of the type miRNA3. ( B ) Firefly (fluc) and renilla (rluc) luciferase activities were quantified in a co-transfection experiment, in which the constitutive production of firefly and renilla luciferase from respective expression vectors was inhibited by the indicated expression vector bearing a tet-regulated miRNA3 cassette. Measured luciferase activities were normalized to the present fluorescence intensity of eGFP, which was expressed under control of P CMV from an additional co-transfected expression plasmid. Structure of tandem expression vectors is described in (A) FL-B: expression vector with miRNA3(FL-B) under control of P tet–1 . RL-A, expression vector with miRNA3(RL-A) under control of P tet–1 ; FL-B + RL-A, co-transfection of two expression vectors containing either miRNA3(FL-B) or miRNA3(RL-A) under control of P tet–1 . ( C ) Rluc activities were determined in a co-transfection experiment, in which the constitutive production of renilla luciferase was inhibited by the indicated vectors and normalized to fluc activity. RL-A, RL-B, RL-C: expression vectors with a single miRNA3 targeting rluc at a particular sequence (A or B or C) under control of P tet–1 . Tandem bicistronic constructs follow the nomenclature as described in (A). RL-A+ RL-C: co-transfection of two expression vectors containing either a single miRNA3(RL-A) or a single miRNA3(RL-C) under the control of P tet–1 . Figures B and C show means and SEM from multiple samples taken from at least two independent transfection experiments.

    Article Snippet: For simultaneous detection of fluc and rluc mRNA, the following primers and probes were used: fluc forward primer 5′-TGTGGACGAAGTACCGAAAGGT-3′; fluc reverse primer 5′-CTTCTTGGCCTTTATGAGGATCTC-3′; fluc probe 5′-FAM-CCGGAAAACTC-GACGCAAGAAAAATCAG-TAMRA-3′; rluc forward primer 5′-AAAGGTGAAGTTCGT-CGTCCA-3′; rluc reverse primer 5′-CAACGTCAGGTTTACCACCTTTT-3′; rluc probe 5′-HEX-CATTATCATGGCCTCGTGAAATCCCGT-TAMRA-3′ (FAM: 6-carboxy-fluoresceine; HEX: hexachloro-fluoresceine; TAMRA: 6-carboxy-tetramethyl-rhodamine; biomers.net).

    Techniques: Expressing, Sequencing, Luciferase, Cotransfection, Plasmid Preparation, Fluorescence, Transfection, Activity Assay, Construct

    Dose–response analysis of tet-regulated miRNA3-mediated inactivation of firefly luciferase in the Tet-Off cell line HtTA 16-1. ( A ) Schematic representation of sequence elements within the transgenic constructs used for the generation of triple stable HeLa cell lines. P CMV, CMV-Promoter; tTA, tet-dependent transactivator; P tet bi–1, bidirectional tet-regulated promoter; fluc*, firefly luciferase fusion protein; rluc, renilla luciferase; (A) n 1, SV40 polyadenylation signal; (A) n 2, β-globin polyadenylation signal. ( B ) Dose–response analysis of miRNA target gene firefly luciferase (fluc) and renilla luciferase (rluc) activity, mirroring miRNA transcription at various doxycycline (dox) concentrations in cell line HtTA 16-1, measured 72 h after induction with dox and normalized to total protein concentration. Figure B shows means and SEM from multiple samples of at least two independent experiments.

    Journal: Nucleic Acids Research

    Article Title: Quantitative analysis of conditional gene inactivation using rationally designed, tetracycline-controlled miRNAs

    doi: 10.1093/nar/gkq616

    Figure Lengend Snippet: Dose–response analysis of tet-regulated miRNA3-mediated inactivation of firefly luciferase in the Tet-Off cell line HtTA 16-1. ( A ) Schematic representation of sequence elements within the transgenic constructs used for the generation of triple stable HeLa cell lines. P CMV, CMV-Promoter; tTA, tet-dependent transactivator; P tet bi–1, bidirectional tet-regulated promoter; fluc*, firefly luciferase fusion protein; rluc, renilla luciferase; (A) n 1, SV40 polyadenylation signal; (A) n 2, β-globin polyadenylation signal. ( B ) Dose–response analysis of miRNA target gene firefly luciferase (fluc) and renilla luciferase (rluc) activity, mirroring miRNA transcription at various doxycycline (dox) concentrations in cell line HtTA 16-1, measured 72 h after induction with dox and normalized to total protein concentration. Figure B shows means and SEM from multiple samples of at least two independent experiments.

    Article Snippet: For simultaneous detection of fluc and rluc mRNA, the following primers and probes were used: fluc forward primer 5′-TGTGGACGAAGTACCGAAAGGT-3′; fluc reverse primer 5′-CTTCTTGGCCTTTATGAGGATCTC-3′; fluc probe 5′-FAM-CCGGAAAACTC-GACGCAAGAAAAATCAG-TAMRA-3′; rluc forward primer 5′-AAAGGTGAAGTTCGT-CGTCCA-3′; rluc reverse primer 5′-CAACGTCAGGTTTACCACCTTTT-3′; rluc probe 5′-HEX-CATTATCATGGCCTCGTGAAATCCCGT-TAMRA-3′ (FAM: 6-carboxy-fluoresceine; HEX: hexachloro-fluoresceine; TAMRA: 6-carboxy-tetramethyl-rhodamine; biomers.net).

    Techniques: Luciferase, Sequencing, Transgenic Assay, Construct, Activity Assay, Protein Concentration

    Recovery kinetics of target gene expression after the termination of the tet-regulated miRNA3-mediated gene knockdown in the Tet-Off cell line HtTA 16-1. (A+D) Tet-regulated co-expression of mi RNA3(FL-B) and rluc in the cell line HtTA16-1 (utilizing the Tet Off system) was kept activated for 1 week (red), 2 weeks (black) and 4 weeks (green). Then, tet-regulated gene expression was switched off, by addition of dox (500 ng/ml), and rluc ( A ) and fluc ( D ) activity measured at indicated time points over a period of 192 h. Both luciferase activities were normalized to total protein concentration. The boxed area marks the time period analysed in B, C and E. (B+C+E) Quantification of relative rluc ( B ) and fluc ( E ) mRNA concentrations and the concentration of mature miRNA ( C ) within a period of 72 h after tet-regulated gene expression, that has been activated for 2 weeks, was switched off. The mRNA and miRNA concentrations were normalized to the concentration of β-actin mRNA In (E), 100% represents the mRNA concentration in cells expressing no miRNA. Therefore, the rel. fluc mRNA concentration mirrors the knockdown efficiency at respective time points. Figures show means and SEM of multiple samples from two independent experiments. ( F ) Recovery of fluc activity after miRNA3(FL-B) knockdown in cell populations with different division rates. In cell line HtTA 16-1, miRNA expression was activated by growing the cells in the absence of dox for 10 days. After subsequent addition of dox to the tissue culture medium (500 ng/ml) to terminate tet-regulated miRNA3(FL-B) expression, cells were divided into two populations. In one population, the cell cycle was artificially elongated to 48 h by the use of S-phase blocker thymidine (+thymidine, black). In the other population (–thymidine, white), cell division rate was left unaltered at 24 h, serving as a control population. Figure shows fluc activities (rlu/µg total protein) at Days 1, 5 and 9 normalized to a control experiment, in which fluc activities of the same time points were determined in both respective cell populations, that were never subjected to a miRNA-based knockdown of fluc expression.

    Journal: Nucleic Acids Research

    Article Title: Quantitative analysis of conditional gene inactivation using rationally designed, tetracycline-controlled miRNAs

    doi: 10.1093/nar/gkq616

    Figure Lengend Snippet: Recovery kinetics of target gene expression after the termination of the tet-regulated miRNA3-mediated gene knockdown in the Tet-Off cell line HtTA 16-1. (A+D) Tet-regulated co-expression of mi RNA3(FL-B) and rluc in the cell line HtTA16-1 (utilizing the Tet Off system) was kept activated for 1 week (red), 2 weeks (black) and 4 weeks (green). Then, tet-regulated gene expression was switched off, by addition of dox (500 ng/ml), and rluc ( A ) and fluc ( D ) activity measured at indicated time points over a period of 192 h. Both luciferase activities were normalized to total protein concentration. The boxed area marks the time period analysed in B, C and E. (B+C+E) Quantification of relative rluc ( B ) and fluc ( E ) mRNA concentrations and the concentration of mature miRNA ( C ) within a period of 72 h after tet-regulated gene expression, that has been activated for 2 weeks, was switched off. The mRNA and miRNA concentrations were normalized to the concentration of β-actin mRNA In (E), 100% represents the mRNA concentration in cells expressing no miRNA. Therefore, the rel. fluc mRNA concentration mirrors the knockdown efficiency at respective time points. Figures show means and SEM of multiple samples from two independent experiments. ( F ) Recovery of fluc activity after miRNA3(FL-B) knockdown in cell populations with different division rates. In cell line HtTA 16-1, miRNA expression was activated by growing the cells in the absence of dox for 10 days. After subsequent addition of dox to the tissue culture medium (500 ng/ml) to terminate tet-regulated miRNA3(FL-B) expression, cells were divided into two populations. In one population, the cell cycle was artificially elongated to 48 h by the use of S-phase blocker thymidine (+thymidine, black). In the other population (–thymidine, white), cell division rate was left unaltered at 24 h, serving as a control population. Figure shows fluc activities (rlu/µg total protein) at Days 1, 5 and 9 normalized to a control experiment, in which fluc activities of the same time points were determined in both respective cell populations, that were never subjected to a miRNA-based knockdown of fluc expression.

    Article Snippet: For simultaneous detection of fluc and rluc mRNA, the following primers and probes were used: fluc forward primer 5′-TGTGGACGAAGTACCGAAAGGT-3′; fluc reverse primer 5′-CTTCTTGGCCTTTATGAGGATCTC-3′; fluc probe 5′-FAM-CCGGAAAACTC-GACGCAAGAAAAATCAG-TAMRA-3′; rluc forward primer 5′-AAAGGTGAAGTTCGT-CGTCCA-3′; rluc reverse primer 5′-CAACGTCAGGTTTACCACCTTTT-3′; rluc probe 5′-HEX-CATTATCATGGCCTCGTGAAATCCCGT-TAMRA-3′ (FAM: 6-carboxy-fluoresceine; HEX: hexachloro-fluoresceine; TAMRA: 6-carboxy-tetramethyl-rhodamine; biomers.net).

    Techniques: Expressing, Activity Assay, Luciferase, Protein Concentration, Concentration Assay

    Outcome of patients according to pre-HSCT BAALC / ABL1 copy numbers, high vs low, 0. 14 cut, (A) Cumulative Incidence of Relapse and (B) Overall Survival for the entire set (n=82) and (C) Cumulative Incidence of relapse and (D) Overall Survival in patients with a normal karyotype (n=38).

    Journal: Oncotarget

    Article Title: High BAALC copy numbers in peripheral blood prior to allogeneic transplantation predict early relapse in acute myeloid leukemia patients

    doi: 10.18632/oncotarget.21322

    Figure Lengend Snippet: Outcome of patients according to pre-HSCT BAALC / ABL1 copy numbers, high vs low, 0. 14 cut, (A) Cumulative Incidence of Relapse and (B) Overall Survival for the entire set (n=82) and (C) Cumulative Incidence of relapse and (D) Overall Survival in patients with a normal karyotype (n=38).

    Article Snippet: Primers and probe sequences for ABL1 copy number assessment (Biomers, Ulm, Germany) are shown in the . ddPCR was performed on a QX100 platform (BioRad) and QuantaSoft software (Biorad) was used for raw data processing.

    Techniques:

    Comparison of absolute BAALC / ABL1 copy numbers in AML patients pre-HSCT (n=82) and healthy controls (n=7)

    Journal: Oncotarget

    Article Title: High BAALC copy numbers in peripheral blood prior to allogeneic transplantation predict early relapse in acute myeloid leukemia patients

    doi: 10.18632/oncotarget.21322

    Figure Lengend Snippet: Comparison of absolute BAALC / ABL1 copy numbers in AML patients pre-HSCT (n=82) and healthy controls (n=7)

    Article Snippet: Primers and probe sequences for ABL1 copy number assessment (Biomers, Ulm, Germany) are shown in the . ddPCR was performed on a QX100 platform (BioRad) and QuantaSoft software (Biorad) was used for raw data processing.

    Techniques:

    Time from HSCT to relapse according to high (median 78, range 19-244 days) or low (median 116, range 27-543 days) absolute pre-HSCT BAALC / ABL1 copy numbers in relapsed patients (n=28)

    Journal: Oncotarget

    Article Title: High BAALC copy numbers in peripheral blood prior to allogeneic transplantation predict early relapse in acute myeloid leukemia patients

    doi: 10.18632/oncotarget.21322

    Figure Lengend Snippet: Time from HSCT to relapse according to high (median 78, range 19-244 days) or low (median 116, range 27-543 days) absolute pre-HSCT BAALC / ABL1 copy numbers in relapsed patients (n=28)

    Article Snippet: Primers and probe sequences for ABL1 copy number assessment (Biomers, Ulm, Germany) are shown in the . ddPCR was performed on a QX100 platform (BioRad) and QuantaSoft software (Biorad) was used for raw data processing.

    Techniques:

    SPR interaction analyses applying the aptamers PA#2/8 and PA#2/8[S1-58] as analyte. Biacore X100 / sensor chip CAP / ligand: biotinylated native Protein A with immobilization level of ~600 RU / analyte: 5’-fluorescein-labeled aptamer PA#2/8 (A) or truncated variant PA#2/8[S1-58] (C) with different concentrations (250–8000 nM, 2000 nM in triplicate). Double-referenced sensorgrams are shown (blank reference surface without Protein A, buffer injection). Black lines represent the fit to 1:1 binding model. The corresponding plots (B, D) of steady-state binding from the end of the association phases against analyte concentration are used to calculate the steady-state affinity.

    Journal: PLoS ONE

    Article Title: In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

    doi: 10.1371/journal.pone.0134403

    Figure Lengend Snippet: SPR interaction analyses applying the aptamers PA#2/8 and PA#2/8[S1-58] as analyte. Biacore X100 / sensor chip CAP / ligand: biotinylated native Protein A with immobilization level of ~600 RU / analyte: 5’-fluorescein-labeled aptamer PA#2/8 (A) or truncated variant PA#2/8[S1-58] (C) with different concentrations (250–8000 nM, 2000 nM in triplicate). Double-referenced sensorgrams are shown (blank reference surface without Protein A, buffer injection). Black lines represent the fit to 1:1 binding model. The corresponding plots (B, D) of steady-state binding from the end of the association phases against analyte concentration are used to calculate the steady-state affinity.

    Article Snippet: The following primers were used for amplification of the oligonucleotides during the aptamer selection process and were synthesized by biomers.net (Germany): AP10: 5‘-ATACCAGCTTATTCAATT-3‘ , AP60: the modified variant of AP10 with 5’-fluorescein, AP30: 5’-CTAACTGATTACGATTGT-3’ , and TER-AP30: the modified variant of AP30 with 5’-poly-dA20 -HEGL.

    Techniques: SPR Assay, Chromatin Immunoprecipitation, Labeling, Variant Assay, Injection, Binding Assay, Concentration Assay

    Most abundant aptamer sequences in the selected aptamer pool. Seven groups with 3–8 homologous sequences (#: number of homologous sequences) were identified among the sequenced aptamer clones. The representative aptamer clone of each group is shown. The specific primer binding sites at the 5’- and 3’-end of the aptamer clones are colored in red and blue, respectively.

    Journal: PLoS ONE

    Article Title: In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

    doi: 10.1371/journal.pone.0134403

    Figure Lengend Snippet: Most abundant aptamer sequences in the selected aptamer pool. Seven groups with 3–8 homologous sequences (#: number of homologous sequences) were identified among the sequenced aptamer clones. The representative aptamer clone of each group is shown. The specific primer binding sites at the 5’- and 3’-end of the aptamer clones are colored in red and blue, respectively.

    Article Snippet: The following primers were used for amplification of the oligonucleotides during the aptamer selection process and were synthesized by biomers.net (Germany): AP10: 5‘-ATACCAGCTTATTCAATT-3‘ , AP60: the modified variant of AP10 with 5’-fluorescein, AP30: 5’-CTAACTGATTACGATTGT-3’ , and TER-AP30: the modified variant of AP30 with 5’-poly-dA20 -HEGL.

    Techniques: Clone Assay, Binding Assay

    SPR interaction analysis regarding the affinity of the truncated aptamer PA#2/8[S1-58]. Biacore X100 / sensor chip CAP / ligand: 3'-biotinylated truncated aptamer PA#2/8[S1-58] with immobilization level of 1030 RU / analyte: recombinant Protein A with different concentrations (50–2500 nM, 1000 nM in duplicate). Double-referenced sensorgram (A) is shown (reference surface modified with unselected SELEX library, buffer injection). Black lines represent the fit to bivalent analyte binding model. The corresponding plot (B) of steady-state binding from the end of the association phases against analyte concentration is used to calculate the steady-state affinity.

    Journal: PLoS ONE

    Article Title: In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

    doi: 10.1371/journal.pone.0134403

    Figure Lengend Snippet: SPR interaction analysis regarding the affinity of the truncated aptamer PA#2/8[S1-58]. Biacore X100 / sensor chip CAP / ligand: 3'-biotinylated truncated aptamer PA#2/8[S1-58] with immobilization level of 1030 RU / analyte: recombinant Protein A with different concentrations (50–2500 nM, 1000 nM in duplicate). Double-referenced sensorgram (A) is shown (reference surface modified with unselected SELEX library, buffer injection). Black lines represent the fit to bivalent analyte binding model. The corresponding plot (B) of steady-state binding from the end of the association phases against analyte concentration is used to calculate the steady-state affinity.

    Article Snippet: The following primers were used for amplification of the oligonucleotides during the aptamer selection process and were synthesized by biomers.net (Germany): AP10: 5‘-ATACCAGCTTATTCAATT-3‘ , AP60: the modified variant of AP10 with 5’-fluorescein, AP30: 5’-CTAACTGATTACGATTGT-3’ , and TER-AP30: the modified variant of AP30 with 5’-poly-dA20 -HEGL.

    Techniques: SPR Assay, Chromatin Immunoprecipitation, Recombinant, Modification, Injection, Binding Assay, Concentration Assay

    Binding abilities of the truncated aptamer variants in comparison to the full-length aptamer PA#2/8 to Protein A. Bead-based binding assays were performed using Protein A/Strep-MB and fluorescein-labeled ssDNA. Target-bound aptamers were eluted and quantified.

    Journal: PLoS ONE

    Article Title: In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

    doi: 10.1371/journal.pone.0134403

    Figure Lengend Snippet: Binding abilities of the truncated aptamer variants in comparison to the full-length aptamer PA#2/8 to Protein A. Bead-based binding assays were performed using Protein A/Strep-MB and fluorescein-labeled ssDNA. Target-bound aptamers were eluted and quantified.

    Article Snippet: The following primers were used for amplification of the oligonucleotides during the aptamer selection process and were synthesized by biomers.net (Germany): AP10: 5‘-ATACCAGCTTATTCAATT-3‘ , AP60: the modified variant of AP10 with 5’-fluorescein, AP30: 5’-CTAACTGATTACGATTGT-3’ , and TER-AP30: the modified variant of AP30 with 5’-poly-dA20 -HEGL.

    Techniques: Binding Assay, Labeling

    Full-length aptamer PA#2/8 and truncated aptamer variants. The primer binding sites at the 5’- and 3’-end are colored in red and blue, respectively. The G-stretches in the internal sequence region are highlighted in grey.

    Journal: PLoS ONE

    Article Title: In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

    doi: 10.1371/journal.pone.0134403

    Figure Lengend Snippet: Full-length aptamer PA#2/8 and truncated aptamer variants. The primer binding sites at the 5’- and 3’-end are colored in red and blue, respectively. The G-stretches in the internal sequence region are highlighted in grey.

    Article Snippet: The following primers were used for amplification of the oligonucleotides during the aptamer selection process and were synthesized by biomers.net (Germany): AP10: 5‘-ATACCAGCTTATTCAATT-3‘ , AP60: the modified variant of AP10 with 5’-fluorescein, AP30: 5’-CTAACTGATTACGATTGT-3’ , and TER-AP30: the modified variant of AP30 with 5’-poly-dA20 -HEGL.

    Techniques: Binding Assay, Sequencing

    SPR interaction analyses regarding the specificity of aptamer PA#2/8. Biacore X100 / sensor chip CAP / ligand: 3'-biotinylated aptamer PA#2/8 with immobilization level of 1000–1200 RU / analyte: different proteins with a concentration of 1000 nM each (recombinant Protein A, Protein G, and Protein L in triplicate; HSA, BSA, and human Thrombin in duplicate). Double-referenced sensorgrams (A) are shown (reference surface modified with unselected SELEX library, buffer injection). Bar graph (B) of binding levels of the different proteins from the end of the association phases (after 300 s of injection) is presented.

    Journal: PLoS ONE

    Article Title: In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

    doi: 10.1371/journal.pone.0134403

    Figure Lengend Snippet: SPR interaction analyses regarding the specificity of aptamer PA#2/8. Biacore X100 / sensor chip CAP / ligand: 3'-biotinylated aptamer PA#2/8 with immobilization level of 1000–1200 RU / analyte: different proteins with a concentration of 1000 nM each (recombinant Protein A, Protein G, and Protein L in triplicate; HSA, BSA, and human Thrombin in duplicate). Double-referenced sensorgrams (A) are shown (reference surface modified with unselected SELEX library, buffer injection). Bar graph (B) of binding levels of the different proteins from the end of the association phases (after 300 s of injection) is presented.

    Article Snippet: The following primers were used for amplification of the oligonucleotides during the aptamer selection process and were synthesized by biomers.net (Germany): AP10: 5‘-ATACCAGCTTATTCAATT-3‘ , AP60: the modified variant of AP10 with 5’-fluorescein, AP30: 5’-CTAACTGATTACGATTGT-3’ , and TER-AP30: the modified variant of AP30 with 5’-poly-dA20 -HEGL.

    Techniques: SPR Assay, Chromatin Immunoprecipitation, Concentration Assay, Recombinant, Modification, Injection, Binding Assay

    SPR interaction analyses regarding the aptamer binding site in Protein A. Biacore X100 / sensor chip CAP / ligand: biotinylated Protein A with immobilization level of ~560 RU / two-step analyte binding without regeneration in between, (A-B) analyte 1 = sample 1: human IgG, IgG-Fc fragment, IgG-Fab fragment with a concentration of 1000 nM each, or buffer, (C-D) analyte 1 = sample 1: concentration series of human IgG-Fc in the range of 0–1000 nM, (A-D) analyte 2 = sample 2: 2000 nM 5’-fluorescein-labeled aptamer PA#2/8 or buffer. Double-referenced sensorgrams are shown (blank reference surface without Protein A, buffer injection). Binding of sample 1 followed by sample 2 is shown in (A) and (C) with alignment to injection start of sample 1. In (B) and (D) only binding of sample 2 with alignment to injection start of sample 2 is shown.

    Journal: PLoS ONE

    Article Title: In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

    doi: 10.1371/journal.pone.0134403

    Figure Lengend Snippet: SPR interaction analyses regarding the aptamer binding site in Protein A. Biacore X100 / sensor chip CAP / ligand: biotinylated Protein A with immobilization level of ~560 RU / two-step analyte binding without regeneration in between, (A-B) analyte 1 = sample 1: human IgG, IgG-Fc fragment, IgG-Fab fragment with a concentration of 1000 nM each, or buffer, (C-D) analyte 1 = sample 1: concentration series of human IgG-Fc in the range of 0–1000 nM, (A-D) analyte 2 = sample 2: 2000 nM 5’-fluorescein-labeled aptamer PA#2/8 or buffer. Double-referenced sensorgrams are shown (blank reference surface without Protein A, buffer injection). Binding of sample 1 followed by sample 2 is shown in (A) and (C) with alignment to injection start of sample 1. In (B) and (D) only binding of sample 2 with alignment to injection start of sample 2 is shown.

    Article Snippet: The following primers were used for amplification of the oligonucleotides during the aptamer selection process and were synthesized by biomers.net (Germany): AP10: 5‘-ATACCAGCTTATTCAATT-3‘ , AP60: the modified variant of AP10 with 5’-fluorescein, AP30: 5’-CTAACTGATTACGATTGT-3’ , and TER-AP30: the modified variant of AP30 with 5’-poly-dA20 -HEGL.

    Techniques: SPR Assay, Binding Assay, Chromatin Immunoprecipitation, Concentration Assay, Labeling, Injection

    Individual binding abilities of the most abundant aptamer sequences to Protein A. The representative aptamer clones of the seven sequence groups were tested for their binding ability to Protein A in comparison to the selected aptamer pool and the unselected SELEX library. Bead-based binding assays were performed using Protein A/Strep-MB and fluorescein-labeled ssDNA. Target-bound aptamers were eluted and quantified.

    Journal: PLoS ONE

    Article Title: In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

    doi: 10.1371/journal.pone.0134403

    Figure Lengend Snippet: Individual binding abilities of the most abundant aptamer sequences to Protein A. The representative aptamer clones of the seven sequence groups were tested for their binding ability to Protein A in comparison to the selected aptamer pool and the unselected SELEX library. Bead-based binding assays were performed using Protein A/Strep-MB and fluorescein-labeled ssDNA. Target-bound aptamers were eluted and quantified.

    Article Snippet: The following primers were used for amplification of the oligonucleotides during the aptamer selection process and were synthesized by biomers.net (Germany): AP10: 5‘-ATACCAGCTTATTCAATT-3‘ , AP60: the modified variant of AP10 with 5’-fluorescein, AP30: 5’-CTAACTGATTACGATTGT-3’ , and TER-AP30: the modified variant of AP30 with 5’-poly-dA20 -HEGL.

    Techniques: Binding Assay, Clone Assay, Sequencing, Labeling

    Potential secondary structure of aptamer PA#2/8. The primer binding sites (18 nt each) at the 5’- and 3’-end are highlighted in red and blue, respectively. The four G-stretches in the intern sequence region are highlighted in grey.

    Journal: PLoS ONE

    Article Title: In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

    doi: 10.1371/journal.pone.0134403

    Figure Lengend Snippet: Potential secondary structure of aptamer PA#2/8. The primer binding sites (18 nt each) at the 5’- and 3’-end are highlighted in red and blue, respectively. The four G-stretches in the intern sequence region are highlighted in grey.

    Article Snippet: The following primers were used for amplification of the oligonucleotides during the aptamer selection process and were synthesized by biomers.net (Germany): AP10: 5‘-ATACCAGCTTATTCAATT-3‘ , AP60: the modified variant of AP10 with 5’-fluorescein, AP30: 5’-CTAACTGATTACGATTGT-3’ , and TER-AP30: the modified variant of AP30 with 5’-poly-dA20 -HEGL.

    Techniques: Binding Assay, Sequencing

    Overview of calculated dissociation constants ( K D ) of aptamer PA#2/8 and its truncated variants. Results of the applied assays with different measuring principles were compared.

    Journal: PLoS ONE

    Article Title: In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

    doi: 10.1371/journal.pone.0134403

    Figure Lengend Snippet: Overview of calculated dissociation constants ( K D ) of aptamer PA#2/8 and its truncated variants. Results of the applied assays with different measuring principles were compared.

    Article Snippet: The following primers were used for amplification of the oligonucleotides during the aptamer selection process and were synthesized by biomers.net (Germany): AP10: 5‘-ATACCAGCTTATTCAATT-3‘ , AP60: the modified variant of AP10 with 5’-fluorescein, AP30: 5’-CTAACTGATTACGATTGT-3’ , and TER-AP30: the modified variant of AP30 with 5’-poly-dA20 -HEGL.

    Techniques:

    Binding curve of aptamer PA#2/8 obtained by bead-based binding assays. A constant number of Protein A/Strep-MB in each assay and a concentration series of the fluorescein-labeled aptamer were used. The dissociation constant ( K D ) of 1.06 ±0.2 μM was calculated by nonlinear regression analysis.

    Journal: PLoS ONE

    Article Title: In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

    doi: 10.1371/journal.pone.0134403

    Figure Lengend Snippet: Binding curve of aptamer PA#2/8 obtained by bead-based binding assays. A constant number of Protein A/Strep-MB in each assay and a concentration series of the fluorescein-labeled aptamer were used. The dissociation constant ( K D ) of 1.06 ±0.2 μM was calculated by nonlinear regression analysis.

    Article Snippet: The following primers were used for amplification of the oligonucleotides during the aptamer selection process and were synthesized by biomers.net (Germany): AP10: 5‘-ATACCAGCTTATTCAATT-3‘ , AP60: the modified variant of AP10 with 5’-fluorescein, AP30: 5’-CTAACTGATTACGATTGT-3’ , and TER-AP30: the modified variant of AP30 with 5’-poly-dA20 -HEGL.

    Techniques: Binding Assay, Concentration Assay, Labeling

    SPR interaction analyses concerning the immobilization orientation of aptamer PA#2/8. Biacore X100 / sensor chip CAP / ligand: 5’-biotinylated aptamer PA#2/8 (A) or 3'-biotinylated aptamer PA#2/8 (B) / analyte: recombinant Protein A with different concentrations (50–2500 nM, 1000 nM in duplicate). Double-referenced sensorgrams are shown (reference surface modified with unselected SELEX library, buffer injection). Black lines represent the fit to bivalent analyte binding model.

    Journal: PLoS ONE

    Article Title: In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

    doi: 10.1371/journal.pone.0134403

    Figure Lengend Snippet: SPR interaction analyses concerning the immobilization orientation of aptamer PA#2/8. Biacore X100 / sensor chip CAP / ligand: 5’-biotinylated aptamer PA#2/8 (A) or 3'-biotinylated aptamer PA#2/8 (B) / analyte: recombinant Protein A with different concentrations (50–2500 nM, 1000 nM in duplicate). Double-referenced sensorgrams are shown (reference surface modified with unselected SELEX library, buffer injection). Black lines represent the fit to bivalent analyte binding model.

    Article Snippet: The following primers were used for amplification of the oligonucleotides during the aptamer selection process and were synthesized by biomers.net (Germany): AP10: 5‘-ATACCAGCTTATTCAATT-3‘ , AP60: the modified variant of AP10 with 5’-fluorescein, AP30: 5’-CTAACTGATTACGATTGT-3’ , and TER-AP30: the modified variant of AP30 with 5’-poly-dA20 -HEGL.

    Techniques: SPR Assay, Chromatin Immunoprecipitation, Recombinant, Modification, Injection, Binding Assay

    Aptamer—Protein A interactions analyzed by MST. Binding curves for the interactions of fluorescently labeled aptamer PA#2/8 (A, D) or its truncated variants PA#2/8[S1-58] (B, E) and PA#2/8[S1-43] (C, F) with recombinant or native Protein A are shown. BSA was used as negative control (A). The aptamer concentration was kept constant at 50 nM for each interaction analysis and the protein was titrated in the range from 1.69 to 55,555 nM of recombinant Protein A and from 0.33 to 10,820 nM of native Protein A, respectively. The binding data were fitted, and the dissociation constants ( K D ) were calculated.

    Journal: PLoS ONE

    Article Title: In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

    doi: 10.1371/journal.pone.0134403

    Figure Lengend Snippet: Aptamer—Protein A interactions analyzed by MST. Binding curves for the interactions of fluorescently labeled aptamer PA#2/8 (A, D) or its truncated variants PA#2/8[S1-58] (B, E) and PA#2/8[S1-43] (C, F) with recombinant or native Protein A are shown. BSA was used as negative control (A). The aptamer concentration was kept constant at 50 nM for each interaction analysis and the protein was titrated in the range from 1.69 to 55,555 nM of recombinant Protein A and from 0.33 to 10,820 nM of native Protein A, respectively. The binding data were fitted, and the dissociation constants ( K D ) were calculated.

    Article Snippet: The following primers were used for amplification of the oligonucleotides during the aptamer selection process and were synthesized by biomers.net (Germany): AP10: 5‘-ATACCAGCTTATTCAATT-3‘ , AP60: the modified variant of AP10 with 5’-fluorescein, AP30: 5’-CTAACTGATTACGATTGT-3’ , and TER-AP30: the modified variant of AP30 with 5’-poly-dA20 -HEGL.

    Techniques: Microscale Thermophoresis, Binding Assay, Labeling, Recombinant, Negative Control, Concentration Assay

    SPR interaction analyses regarding the affinity of aptamer PA#2/8. Biacore X100 / sensor chip CAP / ligand: 3'-biotinylated aptamer PA#2/8 with immobilization levels of 1086 RU (A), 1158 RU (C), 506 RU (E), 316 RU (F) / analyte: recombinant and native Protein A with different concentrations (10–5000 nM, 1000 nM in triplicate) / single-cycle mode (H) with an aptamer level of 516 RU and sequential injections of five ascending concentrations of recombinant Protein A (62, 185, 556, 1667, 5000 nM) as triplicate. Double-referenced sensorgrams are shown (reference surface modified with unselected SELEX library, buffer injection). Black lines represent the fit to bivalent analyte binding model. The corresponding plots (B, D, G, I) of steady-state binding from the end of the association phases against analyte concentration were used to calculate the steady-state affinity.

    Journal: PLoS ONE

    Article Title: In vitro Selection and Interaction Studies of a DNA Aptamer Targeting Protein A

    doi: 10.1371/journal.pone.0134403

    Figure Lengend Snippet: SPR interaction analyses regarding the affinity of aptamer PA#2/8. Biacore X100 / sensor chip CAP / ligand: 3'-biotinylated aptamer PA#2/8 with immobilization levels of 1086 RU (A), 1158 RU (C), 506 RU (E), 316 RU (F) / analyte: recombinant and native Protein A with different concentrations (10–5000 nM, 1000 nM in triplicate) / single-cycle mode (H) with an aptamer level of 516 RU and sequential injections of five ascending concentrations of recombinant Protein A (62, 185, 556, 1667, 5000 nM) as triplicate. Double-referenced sensorgrams are shown (reference surface modified with unselected SELEX library, buffer injection). Black lines represent the fit to bivalent analyte binding model. The corresponding plots (B, D, G, I) of steady-state binding from the end of the association phases against analyte concentration were used to calculate the steady-state affinity.

    Article Snippet: The following primers were used for amplification of the oligonucleotides during the aptamer selection process and were synthesized by biomers.net (Germany): AP10: 5‘-ATACCAGCTTATTCAATT-3‘ , AP60: the modified variant of AP10 with 5’-fluorescein, AP30: 5’-CTAACTGATTACGATTGT-3’ , and TER-AP30: the modified variant of AP30 with 5’-poly-dA20 -HEGL.

    Techniques: SPR Assay, Chromatin Immunoprecipitation, Recombinant, Modification, Injection, Binding Assay, Concentration Assay

    ClustalW [ 23 ] comparison of the sequences for kanamycin binding aptamers derived from different types of SELEX. #3_18 (gr. 7): aptamer developed by Capture-SELEX as described here. Kana18: aptamer developed by Song et al., 2011 [ 27 ] using affinity chromatography with kanamycin-immobilized sepharose beads. Fixed regions are marked with green (5′-primer binding regions), blue (3′-primer binding regions), and magenta (docking sequence). Random regions are printed in black. Red: binding region as assumed by Song et al., 2011 [ 27 ] and underlined: stem-loop forming sequence as given in [ 27 ].

    Journal: Journal of Analytical Methods in Chemistry

    Article Title: Capture-SELEX: Selection of DNA Aptamers for Aminoglycoside Antibiotics

    doi: 10.1155/2012/415697

    Figure Lengend Snippet: ClustalW [ 23 ] comparison of the sequences for kanamycin binding aptamers derived from different types of SELEX. #3_18 (gr. 7): aptamer developed by Capture-SELEX as described here. Kana18: aptamer developed by Song et al., 2011 [ 27 ] using affinity chromatography with kanamycin-immobilized sepharose beads. Fixed regions are marked with green (5′-primer binding regions), blue (3′-primer binding regions), and magenta (docking sequence). Random regions are printed in black. Red: binding region as assumed by Song et al., 2011 [ 27 ] and underlined: stem-loop forming sequence as given in [ 27 ].

    Article Snippet: The following primers were used for amplification of the oligonucleotides during the aptamer selection process and were synthesized by biomers.net (Germany): AP10:5′-ATACCAGCTTATTCAATT-3′, AP60: the modified variant of AP10 with 5′-fluorescein, AP20:5′-AGATTGCACTTACTATCT-3′, and TER-AP20:the modified variant of AP20 with 5′-poly-dA20 -HEGL [ ].

    Techniques: Binding Assay, Derivative Assay, Affinity Chromatography, Sequencing

    Affinity tests on the representatives of aptamer groups evolved from Capture-SELEX. Affinity tests were performed similar to the Capture-SELEX procedure, and ssDNA was eluted by different concentrations of kanamycin A in selection buffer. Data was fitted by the model of one site direct binding using a rectangular hyperbola for the saturation curve (OriginLab Corporation, OriginPro 8G SR2).

    Journal: Journal of Analytical Methods in Chemistry

    Article Title: Capture-SELEX: Selection of DNA Aptamers for Aminoglycoside Antibiotics

    doi: 10.1155/2012/415697

    Figure Lengend Snippet: Affinity tests on the representatives of aptamer groups evolved from Capture-SELEX. Affinity tests were performed similar to the Capture-SELEX procedure, and ssDNA was eluted by different concentrations of kanamycin A in selection buffer. Data was fitted by the model of one site direct binding using a rectangular hyperbola for the saturation curve (OriginLab Corporation, OriginPro 8G SR2).

    Article Snippet: The following primers were used for amplification of the oligonucleotides during the aptamer selection process and were synthesized by biomers.net (Germany): AP10:5′-ATACCAGCTTATTCAATT-3′, AP60: the modified variant of AP10 with 5′-fluorescein, AP20:5′-AGATTGCACTTACTATCT-3′, and TER-AP20:the modified variant of AP20 with 5′-poly-dA20 -HEGL [ ].

    Techniques: Selection, Binding Assay