Fluorescence anistropy or early FRET methods |
Only one fluorescent label on the DNA is required. |
Fluorescence polarization has a small dynamic range and depends on the sizes of the DNA and protein molecules.
FRET signal depends on the number and position of endogenous fluorescent residues.
Lack of generalizability.
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MB strategy |
An increased dynamic range not limited to the size of molecules or the number and position of endogenous fluorescent residues.
Can be adapted for sensing different DNA-binding proteins by modification of the oligonucleotide binding site.
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Aptamer beacon strategy |
High affinity aptamers can be raised, in principle, for any protein target.
Can be adapted for sensing different proteins by modification of the aptamer sequence.
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Labeling can be quite expensive and interfere with the protein–DNA interaction.
Some designs rely on specific aptamer structural features, reducing generalizability.
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Label-free strategy |
Economical, suitable for high-throughput or low-cost applications. |
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Exonuclease protection strategy |
No need to consider the equilibria between multiple oligonucleotide conformations and the bound and free states of the beacon or aptamer. |
Can be more susceptible to false positives. |