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Investigating the ligand binding mode and selectivity with biophysical methods (A) Chemical structures of probe 8 : TAMRA-labeled β-homo-tripeptide. (B) MST dose-response curves for probe 8 binding to DNMT2. (C) Fluorescence polarization assay for probe 6 binding to native DNMT2 (2 μM), DNMT2 (2 μM) preincubated with SAH (100 μM), DNMT2 (2 μM) with tRNA Asp (10 μM), and various related MTase off-targets (all 2 μM). (D) DNMT2-SAH ITC <t>displacement</t> experiment for compound 3 . SAH was titrated to DNMT2 in the absence resp. presence of compound 3 (100 μM), yielding a significant enthalpy reduction. (E) EMSA assay investigates the competition of hit compounds 1 – 5 with the tRNA substrate. Positive control: tRNA+DNMT2 (band at high molecular weights); negative control: only tRNA (band at low molecular weights). Hit compounds 1 – 5 (100 μM) were added to the DNMT2-tRNA complex (10 + 5 μM) and analyzed by native PAGE. No compound was able to dissociate the DNMT2-tRNA complex. Data are represented as mean ± SEM. Uncropped PAGE images can be found in .
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curve fitting tool (cftool)  (MathWorks Inc)
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Investigating the ligand binding mode and selectivity with biophysical methods (A) Chemical structures of probe 8 : TAMRA-labeled β-homo-tripeptide. (B) MST dose-response curves for probe 8 binding to DNMT2. (C) Fluorescence polarization assay for probe 6 binding to native DNMT2 (2 μM), DNMT2 (2 μM) preincubated with SAH (100 μM), DNMT2 (2 μM) with tRNA Asp (10 μM), and various related MTase off-targets (all 2 μM). (D) DNMT2-SAH ITC <t>displacement</t> experiment for compound 3 . SAH was titrated to DNMT2 in the absence resp. presence of compound 3 (100 μM), yielding a significant enthalpy reduction. (E) EMSA assay investigates the competition of hit compounds 1 – 5 with the tRNA substrate. Positive control: tRNA+DNMT2 (band at high molecular weights); negative control: only tRNA (band at low molecular weights). Hit compounds 1 – 5 (100 μM) were added to the DNMT2-tRNA complex (10 + 5 μM) and analyzed by native PAGE. No compound was able to dissociate the DNMT2-tRNA complex. Data are represented as mean ± SEM. Uncropped PAGE images can be found in .
Curve Fitting Tool (Cftool), supplied by MathWorks Inc, 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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belysa immunoassay curve fitting software  (Millipore)
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Investigating the ligand binding mode and selectivity with biophysical methods (A) Chemical structures of probe 8 : TAMRA-labeled β-homo-tripeptide. (B) MST dose-response curves for probe 8 binding to DNMT2. (C) Fluorescence polarization assay for probe 6 binding to native DNMT2 (2 μM), DNMT2 (2 μM) preincubated with SAH (100 μM), DNMT2 (2 μM) with tRNA Asp (10 μM), and various related MTase off-targets (all 2 μM). (D) DNMT2-SAH ITC <t>displacement</t> experiment for compound 3 . SAH was titrated to DNMT2 in the absence resp. presence of compound 3 (100 μM), yielding a significant enthalpy reduction. (E) EMSA assay investigates the competition of hit compounds 1 – 5 with the tRNA substrate. Positive control: tRNA+DNMT2 (band at high molecular weights); negative control: only tRNA (band at low molecular weights). Hit compounds 1 – 5 (100 μM) were added to the DNMT2-tRNA complex (10 + 5 μM) and analyzed by native PAGE. No compound was able to dissociate the DNMT2-tRNA complex. Data are represented as mean ± SEM. Uncropped PAGE images can be found in .
Belysa Immunoassay Curve Fitting Software, supplied by Millipore, 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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curve fitting tool  (MathWorks Inc)
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Investigating the ligand binding mode and selectivity with biophysical methods (A) Chemical structures of probe 8 : TAMRA-labeled β-homo-tripeptide. (B) MST dose-response curves for probe 8 binding to DNMT2. (C) Fluorescence polarization assay for probe 6 binding to native DNMT2 (2 μM), DNMT2 (2 μM) preincubated with SAH (100 μM), DNMT2 (2 μM) with tRNA Asp (10 μM), and various related MTase off-targets (all 2 μM). (D) DNMT2-SAH ITC <t>displacement</t> experiment for compound 3 . SAH was titrated to DNMT2 in the absence resp. presence of compound 3 (100 μM), yielding a significant enthalpy reduction. (E) EMSA assay investigates the competition of hit compounds 1 – 5 with the tRNA substrate. Positive control: tRNA+DNMT2 (band at high molecular weights); negative control: only tRNA (band at low molecular weights). Hit compounds 1 – 5 (100 μM) were added to the DNMT2-tRNA complex (10 + 5 μM) and analyzed by native PAGE. No compound was able to dissociate the DNMT2-tRNA complex. Data are represented as mean ± SEM. Uncropped PAGE images can be found in .
Curve Fitting Tool, supplied by MathWorks Inc, 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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Investigating the ligand binding mode and selectivity with biophysical methods (A) Chemical structures of probe 8 : TAMRA-labeled β-homo-tripeptide. (B) MST dose-response curves for probe 8 binding to DNMT2. (C) Fluorescence polarization assay for probe 6 binding to native DNMT2 (2 μM), DNMT2 (2 μM) preincubated with SAH (100 μM), DNMT2 (2 μM) with tRNA Asp (10 μM), and various related MTase off-targets (all 2 μM). (D) DNMT2-SAH ITC <t>displacement</t> experiment for compound 3 . SAH was titrated to DNMT2 in the absence resp. presence of compound 3 (100 μM), yielding a significant enthalpy reduction. (E) EMSA assay investigates the competition of hit compounds 1 – 5 with the tRNA substrate. Positive control: tRNA+DNMT2 (band at high molecular weights); negative control: only tRNA (band at low molecular weights). Hit compounds 1 – 5 (100 μM) were added to the DNMT2-tRNA complex (10 + 5 μM) and analyzed by native PAGE. No compound was able to dissociate the DNMT2-tRNA complex. Data are represented as mean ± SEM. Uncropped PAGE images can be found in .
Non Linear Regression Curve Fit Analysis Using Graphpad Prism Software Version 5.01, supplied by GraphPad Software Inc, 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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non-linear curve fitting in graphpad prism  (GraphPad Software Inc)
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GraphPad Software Inc non-linear curve fitting in graphpad prism
Investigating the ligand binding mode and selectivity with biophysical methods (A) Chemical structures of probe 8 : TAMRA-labeled β-homo-tripeptide. (B) MST dose-response curves for probe 8 binding to DNMT2. (C) Fluorescence polarization assay for probe 6 binding to native DNMT2 (2 μM), DNMT2 (2 μM) preincubated with SAH (100 μM), DNMT2 (2 μM) with tRNA Asp (10 μM), and various related MTase off-targets (all 2 μM). (D) DNMT2-SAH ITC <t>displacement</t> experiment for compound 3 . SAH was titrated to DNMT2 in the absence resp. presence of compound 3 (100 μM), yielding a significant enthalpy reduction. (E) EMSA assay investigates the competition of hit compounds 1 – 5 with the tRNA substrate. Positive control: tRNA+DNMT2 (band at high molecular weights); negative control: only tRNA (band at low molecular weights). Hit compounds 1 – 5 (100 μM) were added to the DNMT2-tRNA complex (10 + 5 μM) and analyzed by native PAGE. No compound was able to dissociate the DNMT2-tRNA complex. Data are represented as mean ± SEM. Uncropped PAGE images can be found in .
Non Linear Curve Fitting In Graphpad Prism, supplied by GraphPad Software Inc, 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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non-linear curve fitting  (GraphPad Software Inc)
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Investigating the ligand binding mode and selectivity with biophysical methods (A) Chemical structures of probe 8 : TAMRA-labeled β-homo-tripeptide. (B) MST dose-response curves for probe 8 binding to DNMT2. (C) Fluorescence polarization assay for probe 6 binding to native DNMT2 (2 μM), DNMT2 (2 μM) preincubated with SAH (100 μM), DNMT2 (2 μM) with tRNA Asp (10 μM), and various related MTase off-targets (all 2 μM). (D) DNMT2-SAH ITC <t>displacement</t> experiment for compound 3 . SAH was titrated to DNMT2 in the absence resp. presence of compound 3 (100 μM), yielding a significant enthalpy reduction. (E) EMSA assay investigates the competition of hit compounds 1 – 5 with the tRNA substrate. Positive control: tRNA+DNMT2 (band at high molecular weights); negative control: only tRNA (band at low molecular weights). Hit compounds 1 – 5 (100 μM) were added to the DNMT2-tRNA complex (10 + 5 μM) and analyzed by native PAGE. No compound was able to dissociate the DNMT2-tRNA complex. Data are represented as mean ± SEM. Uncropped PAGE images can be found in .
Non Linear Curve Fitting, supplied by GraphPad Software Inc, 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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nonlinear regression curve fitting  (GraphPad Software Inc)
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Investigating the ligand binding mode and selectivity with biophysical methods (A) Chemical structures of probe 8 : TAMRA-labeled β-homo-tripeptide. (B) MST dose-response curves for probe 8 binding to DNMT2. (C) Fluorescence polarization assay for probe 6 binding to native DNMT2 (2 μM), DNMT2 (2 μM) preincubated with SAH (100 μM), DNMT2 (2 μM) with tRNA Asp (10 μM), and various related MTase off-targets (all 2 μM). (D) DNMT2-SAH ITC <t>displacement</t> experiment for compound 3 . SAH was titrated to DNMT2 in the absence resp. presence of compound 3 (100 μM), yielding a significant enthalpy reduction. (E) EMSA assay investigates the competition of hit compounds 1 – 5 with the tRNA substrate. Positive control: tRNA+DNMT2 (band at high molecular weights); negative control: only tRNA (band at low molecular weights). Hit compounds 1 – 5 (100 μM) were added to the DNMT2-tRNA complex (10 + 5 μM) and analyzed by native PAGE. No compound was able to dissociate the DNMT2-tRNA complex. Data are represented as mean ± SEM. Uncropped PAGE images can be found in .
Nonlinear Regression Curve Fitting, supplied by GraphPad Software Inc, 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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curve-fitting software graphpad prism 10.3.1  (GraphPad Software Inc)
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Investigating the ligand binding mode and selectivity with biophysical methods (A) Chemical structures of probe 8 : TAMRA-labeled β-homo-tripeptide. (B) MST dose-response curves for probe 8 binding to DNMT2. (C) Fluorescence polarization assay for probe 6 binding to native DNMT2 (2 μM), DNMT2 (2 μM) preincubated with SAH (100 μM), DNMT2 (2 μM) with tRNA Asp (10 μM), and various related MTase off-targets (all 2 μM). (D) DNMT2-SAH ITC <t>displacement</t> experiment for compound 3 . SAH was titrated to DNMT2 in the absence resp. presence of compound 3 (100 μM), yielding a significant enthalpy reduction. (E) EMSA assay investigates the competition of hit compounds 1 – 5 with the tRNA substrate. Positive control: tRNA+DNMT2 (band at high molecular weights); negative control: only tRNA (band at low molecular weights). Hit compounds 1 – 5 (100 μM) were added to the DNMT2-tRNA complex (10 + 5 μM) and analyzed by native PAGE. No compound was able to dissociate the DNMT2-tRNA complex. Data are represented as mean ± SEM. Uncropped PAGE images can be found in .
Curve Fitting Software Graphpad Prism 10.3.1, supplied by GraphPad Software Inc, 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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Investigating the ligand binding mode and selectivity with biophysical methods (A) Chemical structures of probe 8 : TAMRA-labeled β-homo-tripeptide. (B) MST dose-response curves for probe 8 binding to DNMT2. (C) Fluorescence polarization assay for probe 6 binding to native DNMT2 (2 μM), DNMT2 (2 μM) preincubated with SAH (100 μM), DNMT2 (2 μM) with tRNA Asp (10 μM), and various related MTase off-targets (all 2 μM). (D) DNMT2-SAH ITC displacement experiment for compound 3 . SAH was titrated to DNMT2 in the absence resp. presence of compound 3 (100 μM), yielding a significant enthalpy reduction. (E) EMSA assay investigates the competition of hit compounds 1 – 5 with the tRNA substrate. Positive control: tRNA+DNMT2 (band at high molecular weights); negative control: only tRNA (band at low molecular weights). Hit compounds 1 – 5 (100 μM) were added to the DNMT2-tRNA complex (10 + 5 μM) and analyzed by native PAGE. No compound was able to dissociate the DNMT2-tRNA complex. Data are represented as mean ± SEM. Uncropped PAGE images can be found in .

Journal: iScience

Article Title: DNA-encoded library screening uncovers potent DNMT2 inhibitors targeting a cryptic allosteric binding site

doi: 10.1016/j.isci.2025.113300

Figure Lengend Snippet: Investigating the ligand binding mode and selectivity with biophysical methods (A) Chemical structures of probe 8 : TAMRA-labeled β-homo-tripeptide. (B) MST dose-response curves for probe 8 binding to DNMT2. (C) Fluorescence polarization assay for probe 6 binding to native DNMT2 (2 μM), DNMT2 (2 μM) preincubated with SAH (100 μM), DNMT2 (2 μM) with tRNA Asp (10 μM), and various related MTase off-targets (all 2 μM). (D) DNMT2-SAH ITC displacement experiment for compound 3 . SAH was titrated to DNMT2 in the absence resp. presence of compound 3 (100 μM), yielding a significant enthalpy reduction. (E) EMSA assay investigates the competition of hit compounds 1 – 5 with the tRNA substrate. Positive control: tRNA+DNMT2 (band at high molecular weights); negative control: only tRNA (band at low molecular weights). Hit compounds 1 – 5 (100 μM) were added to the DNMT2-tRNA complex (10 + 5 μM) and analyzed by native PAGE. No compound was able to dissociate the DNMT2-tRNA complex. Data are represented as mean ± SEM. Uncropped PAGE images can be found in .

Article Snippet: Data analysis and displacement curve fitting were accomplished via the MicroCal PEAQ-ITC Analysis Software.

Techniques: Ligand Binding Assay, Labeling, Binding Assay, Fluorescence, Positive Control, Negative Control, Clear Native PAGE