A DNA-Based Biosensor Assay for the Kinetic Characterization of Ion-Dependent Aptamer Folding and Protein Binding
Abstract
:1. Introduction
2. Results
2.1. Development of the Aptasensor
2.2. Real-Time Kinetics of Aptamer Folding
2.3. Influence of Salt Species on Thrombin-Binding Kinetics
2.4. Specificity of TBA for Thrombin Interaction Allows Broad Dynamic Range
2.5. Immobilized Target for Aptamer Screening
3. Discussion
3.1. Real-Time Folding and Unfolding Rates Coupled to Ion Binding
3.2. Resolution of High-Affinity TBA–Protein Interaction
3.3. Differentiation of Prefolded Aptamer from Induced Fit
3.4. Contribution of Results to Therapeutic and Diagnostic Applications
3.5. Effect of Reversing the Assay Orientation
4. Materials and Methods
4.1. Materials
- TBA: 5′(BBQ)-GGT TGG TGT GGT TGG TTT ATC AGC GTT CGA TGC TTC CGA CTA ATC AGC CAT ATC AGC TTA CGA CTA-3′;
- TBAsc: 5′(BBQ)-GTG TGG TGT GTG TGG TTT ATC AGC GTT CGA TGC TTC CGA CTA ATC AGC CAT ATC AGC TTA CGA CTA-3′;
- HTA: 5′-TTT GGG TTA GGG TTA GGG TTA GGG TTT ATC AGC GTT CGA TGC TTC CGA CTA ATC AGC CAT ATC AGC TTA CGA CTA-3′.
4.2. Covalent Conjugation of Thrombin to cNL-B
4.3. SwitchSENSE Experiments
4.4. Data Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Sample Availability: Sources for Thrombin-binding aptamer and thrombin are stated in Materials & Methods, these samples are not available from the authors. |
Ion | kON (M−1s−1) | kOFF = kU (10−1 s−1) | KD (mM) | kF (s−1) | KF (No Unit) |
---|---|---|---|---|---|
NH4+ | 2.96 ± 0.8 | 3.07 ± 0.3 | 104 ± 40 | 1.18 ± 0.23 | 3.84 ± 0.8 |
K+ | 15.2 ± 1.7 | 1.20 ± 0.01 | 7.89 ± 1.3 | 1.26 ± 0.14 | 10.4 ± 1.1 |
Na+ | - | - | - | - | - |
Li+ | - | - | - | - | - |
Buffer | kON (107 M−1s−1) | kOFF (10−2 s−1) | KD (nM) |
---|---|---|---|
TE140-KCl | 38 ± 1.3 | 5.8 ± 0.1 | 0.15 ± 0.01 |
TE140-NH4Cl | 17 ± 1.0 | 4.8 ± 0.1 | 0.28 ± 0.02 |
TE140-NaCl | 3.3 ± 0.2 | 4.3 ± 0.1 | 1.31 ± 0.12 |
TE140-LiCl | 0.03 ± 0.01 | 6.3 ± 0.4 | 245 ± 94 |
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Ponzo, I.; Möller, F.M.; Daub, H.; Matscheko, N. A DNA-Based Biosensor Assay for the Kinetic Characterization of Ion-Dependent Aptamer Folding and Protein Binding. Molecules 2019, 24, 2877. https://doi.org/10.3390/molecules24162877
Ponzo I, Möller FM, Daub H, Matscheko N. A DNA-Based Biosensor Assay for the Kinetic Characterization of Ion-Dependent Aptamer Folding and Protein Binding. Molecules. 2019; 24(16):2877. https://doi.org/10.3390/molecules24162877
Chicago/Turabian StylePonzo, Irene, Friederike M. Möller, Herwin Daub, and Nena Matscheko. 2019. "A DNA-Based Biosensor Assay for the Kinetic Characterization of Ion-Dependent Aptamer Folding and Protein Binding" Molecules 24, no. 16: 2877. https://doi.org/10.3390/molecules24162877