1. Surpassing Specificity Limits of Nucleic Acid Probes via Cooperativity
Brent C. Satterfield, Matt Bartosiewicz, Jay A.A. West, Michael R. Caplan 
The Journal of Molecular Diagnostics 
Volume 12, Issue 3, Pages (May 2010)
DOI: /jmoldx
Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

2. Figure 1
Mechanism of Tentacle Probes, showing how target can bind only to the capture region (Ccap), only to the detection region (Cdet), or to both the capture and the detection region (Ccoop) or how two target molecules can hybridize with the capture and detection regions independently (Cbi; A), mechanism of Taqman probes (B), and mechanism of Molecular Beacons (C). The Tentacle Probe mechanism is the combination of the molecular beacon (Cdet) and linear probe mechanisms (Ccap), thus allowing all three probe types to be represented by the more comprehensive Tentacle Probe mathematical model.
The Journal of Molecular Diagnostics  , DOI: ( /jmoldx )
Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

3. Figure 2
Probe design and model validation. In all graphs, wild-type predictions are shown with solid line and variant(s) are shown with dashed lines. Wild-type data have solid markers with corresponding empty marker for variant(s) at same concentration. Graphs show Tentacle Probe concentration independence across three orders of magnitude (500 nmol/L, 5 μmol/L, 50 μmol/L) for a genomic B. anthracis assay (A), Tentacle Probe large melting temperature differentials for second genomic B. anthracis assay (B), molecular beacon for Malaria with two mutants (C), and Taqman for Herpes Simplex Virus II (D). All mismatches were SNPs except for the Taqman assay that had two polymorphisms.
The Journal of Molecular Diagnostics  , DOI: ( /jmoldx )
Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

4. Figure 3
Evaluation of specificity based on predicted melting curves for drug-susceptible (solid line, black markers are actual data) and drug-resistant (dashed line, gray markers are actual data) pathogenic S. aureus genotypes for Tentacle Probes (A), Molecular Beacons (B), and Taqman (C).
The Journal of Molecular Diagnostics  , DOI: ( /jmoldx )
Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

5. Figure 4
Biophysics of Tentacle Probe melting temperature differentials. Fraction of target bound to the capture and detection regions cooperatively (solid line) or to the capture region only (dashed line) for both wild-type (A) and variant (B) targets. Enhanced specificity in Tentacle Probes is due to the presence of an energetically favorable alternate state (i.e., binding to the capture region only instead of binding cooperatively to both) in the presence of a mismatched target.
The Journal of Molecular Diagnostics  , DOI: ( /jmoldx )
Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

6. Figure 5
Evaluation of specificity based on concentration dependence for drug-susceptible (filled diamonds, data; solid line, fitted curve) and drug-resistant (empty squares, data; dashed line, fitted curve) pathogenic S. aureus genotypes for Tentacle Probes (A), Molecular Beacons (B), and Taqman (C). Binding above background (horizontal dashed line) results in positives for wild-type and false positives for variant targets. Binding assay was performed with 50 nmol/L each probe. 95% confidence intervals are shown.
The Journal of Molecular Diagnostics  , DOI: ( /jmoldx )
Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

7. Figure 6
Biophysics of Tentacle Probe concentration independence. Figure shows the components of bound Tentacle Probes over a broad spectrum of target concentrations including the fraction of Tentacle Probes with target bound only to the capture region (dotted line) and to the detection region (solid line, barely visible at just above 0) as well as the fraction of probes with two targets bound to the capture and detection regions independently (dashed line). The two vertical black lines defining the approximate concentration independent range are the concentration of Tentacle Probes (left line) and the local concentration for the second binding event created by cooperative binding (right line).
The Journal of Molecular Diagnostics  , DOI: ( /jmoldx )
Copyright © 2010 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions