Skip to main content
. Author manuscript; available in PMC: 2019 Mar 28.
Published in final edited form as: Nat Nanotechnol. 2017 Jan 23;12(4):368–377. doi: 10.1038/nnano.2016.284

Figure 1. Characterization of aptamer-anchor structure on nanotube.

Figure 1.

(a) 6,5 chirality RAP1 aptamer-SWNT response to addition of 3 μM RAP1 protein with schematic representation of aptamer-SWNT construct binding, with DNA anchor (blue), and DNA or RNA aptamer (purple). (b) Nine aptamer-SWNT screen (horizontal axis) against nine protein analytes (vertical axis). Red is sensor fluorescence turn-on, blue is sensor fluorescence turn-off, where off-diagonal elements represent SWNT fluorescence response to non-conjugate (nonspecific) protein-aptamer SWNT pairs, and the diagonal (highlighted by a dashed black line) represents fluorescence response to conjugate (specific) protein-aptamer SWNT pairs. We observe strong turn-on responses (red) for RAP1 protein and HIV1 integrase protein, with normalized fluorescence turn-on responses of (I-Io)/Io = 0.53 and 0.48, respectively. (c) RAP1 (top) aptamer-SWNT constructs with N = 1, 3, or 5 abasic spacers between anchor and aptamer detect RAP1 with a larger fluorescence turn-on response than constructs lacking a spacer. The response for thrombin (bottom), however, is unchanged regardless of spacer incorporation. Results suggest an aptamer equilibrium that fluctuates between a correctly folded aptamer (protein accessible) on the SWNT, and an incorrectly folded aptamer (protein inaccessible) on the SWNT surface Error bars are standard error. (d) Single-molecule TIRF visualization of aptamer-SWNT interaction for Cy3-labeled RAP1. Cy3 tag on Thrombin SWNT sensor is initially quenched (top panel, blue histogram) suggesting the thrombin aptamer is denatured on the SWNT. Addition of ssDNA complementary to the Thrombin aptamer, +cThrombin DNA, de-quenches the Cy3 tag and leads to an increase in visible Cy3 fluorophores (red histogram bars). Conversely, Cy3 tag on RAP1 SWNT sensor is initially de-quenched (bottom panel, blue histogram) suggesting the RAP1 aptamer is properly folded on the SWNT. Addition of ssDNA complementary to the RAP1 aptamer, +cRAP1 DNA, does not change the Cy3 count (red histogram bars). Results suggest a primarily SWNT surface-desorbed RAP1 aptamer, and primary SWNT surface-adsorbed Thrombin aptamer.