Transcription Factor Beacons: Optical Switching Probes Driven by Native Interactions

Transcription factors are essential components of gene regulation, and there is great interest in probing their presence and activity in both academic analysis and clinical diagnostics[1] .  Current methods to address these questions are often time-intensive or require specialized reagents, such as antibodies.  In my talk, I will present the development of simple, convenient probes for the quantitative, rapid detection of active transcription factors and other DNA binding proteins.  These probes, which we term “transcription factor beacons,” comprise a versatile new class of oligonucleotide-based fluorescent “switches”[2] that recognize transcription factors using native binding interactions[3].  This approach simplifies the rational design of beacons for any target transcription factor of interest and allows the probes to have affinity and specificity on the order of natural binding interactions. This design has been put into practice with beacons directed against three diverse human transcription factors, and for all targets we find rapid (minute), specific quantification of nanomolar concentrations, retaining selectivity even in media as complex as crude nuclear extracts. Transcription factor beacons thus represent a convenient, versatile, and readily generalized approach to detect active transcription factors that provide significant advantages over existing methods for the detection of DNA-binding proteins.

References:

1. Darnell, J.E. Transcription factors as targets for cancer therapy.  Nature Reviews Cancer 2, 2002, pp. 740-749.
2. Alexis Vallée-Bélisle. & Kevin W. Plaxco.  Structure-switching biosensors: inspired by Nature.  Current Opinion in Structural Biology 20(4), 2010, pp. 518-526.
3. Ricci, F., Bonham, A.J., Mason, A.C., Reich, N.O., Plaxco, K.W.  Reagentless, Electrochemical Approach for the Specific Detection of Double- and Single-Stranded DNA Binding Proteins.  Analytical Chemistry, 81(4), 2009, pp. 1608–1614.